Summary:

Do you remember that ISIS took Jizya from Christians in Iraq and let them live, but ISIS didn't take Jizya from Yazidis and killed their men and enslaved their women?

Here is the reason:

• According to Salafi Islam (and also according to Imam Shafi'i and Imam Ahmed bin Hanbal), Jizya is allowed only for Christians/Jews/Zoroastrians (who are known as the "people of the Book أهل الكتاب" in Islam).
• But as far as other non-Muslims (like Atheists, Deists, Hindus, Buddhists etc.) are concerned, then they cannot live even by paying Jizya. They either have to accept Islam, or they should be slaughtered.
• Muhammad himself didn't accept Jizya from the polytheists of Arabia but after the revelation of the verse of the sword (i.e. killing all polytheists after 4 months), he forced all of them to accept Islam.

Later, some Muslim jurists like Imam Abu Hanifa and Imam Malik said that it was limited only to the polytheists of Arabia, but as far as the polytheists of the non-Arab world are concerned, they could live by paying Jizya.

But other Muslim jurists like Imam Shafii and Imam Ahmed bin Hanbal (and modern-day Salafists) disagree. According to them, non-Arab non-Muslims also don't have any right to live even through paying Jizya. They either have to accept Islam or they should be slaughtered.

This means that if Salafists form an Islamic State today, then they will kill all non-Muslims like Atheists, Buddhists, Hindus, etc. (accept for Jews/Christians/Magians who can stay alive by paying Jizya). 

Details: 

Quran 9:5:

And when the sacred months have passed, then kill the polytheists wherever you find them and capture them and besiege them and sit in wait for them at every place of ambush. But if they should repent, establish prayer, and give zakah (i.e. if they become Muslims), let them [go] on their way.

The Quranic Verse about killing polytheists has become a problem for Islam apologists, while the writer of the Quran (i.e. Muhammad) ordered to kill “all polytheists” in it if they don't accept Islam. They were not even allowed to stay alive by paying the Jizya (Verse 9:29), which was reserved only for Jews & Christians. This was the main tactic which Muhammad used to spread Islam.

Imam Wahidi recorded under the Tafsir of verse 5:105:

Ibn 'Abbas said: “The Messenger of Allah sent a letter to the people of Hajar, whose chief was Mundhir ibn Sawa, inviting them to Islam, or to pay the Jizyah if they chose not to embrace Islam. When Mundhir ibn Sawa received the letter, he showed it to the Arabs, Jews, Christians, Sabeans and Magians who were around him. They all agreed to pay the Jizyah and disliked embracing Islam. The Messenger of Allah, Allah bless him and give him peace, wrote back to him, saying: 'As for the Arabs, do not accept from them except Islam otherwise they will have nothing but the sword. As for the people of the Book and the Magians, accept the Jizyah from them. When this letter was read to them, the Arabs embraced Islam while the people of the Book and the Magians agreed to pay the Jizyah.

But today Muslims are weaker than other nations, therefore Islam apologists are forced to hide the real face of Islam. They fear if the rest of the world comes to know it, then polytheists are going to kill Muslims as Muhammad used to slaughter the polytheists.

• In the 9th Hijri year (one year before his death), Muhammad got “absolute power” and no one was left there in the entire Arabia who could have opposed him. Thus, then in the 9th Hijri year, Muhammad claimed the revelation of verse 9:5 and made the killing of all polytheists Halal (permissible) for Muslims. 
• The peace treaty which Muhammad signed in the 7th Hijri year (at the time of the victory of Mecca) was not with the whole of Arabia, but only with the tribes living in Mecca and around it.
• Thus, whoever had a covenant, their covenant lasted till the end of the covenant. While the other polytheists, who didn't have any covenant, their killing started after 4 months. 

Allah (i.e. Muhammad) didn't even allow polytheists to stay alive after paying Jizya (i.e. only Jews, Christians and Magians were allowed to live by paying Jizya)

The Quranic verse 9:29 testifies two issues:

1. Firstly, to wage a war against Jews and Christians was not due to the reason that they were fighting Muslims, but it was due to the reason that they didn’t believe in Allah and Muhammad.
2. Secondly, Jizya was limited only to Jews and Christians. 

Quran 9:29:

Fight those people of the Book (Jews and Christians) who do not believe in Allah and the Last Day, do not refrain from what has been prohibited by Allah and His Messenger and do not embrace the religion of truth (Al-Islam), until they pay Jizya (protection tax) with their own hands and feel themselves subdued.

Therefore, Allah (i.e. Muhammad) limited Jizya only to the “People of the Book” (i.e. Jews, Christians and Zoroastrians) in this verse, while polytheists were not even allowed to live after paying the Jizya. Polytheists either had to accept Islam, or they would be killed after 4 months (or till the end of their covenant). 

And then there are traditions which are clear about how Muslims killed even peaceful polytheists after the revelation of this verse:

Sahih Bukhari, Book of Battles (link):

Narrated Jarir: In the Pre-lslamic Period of Ignorance there was a house called Dhu-l-Khalasa or Al-Ka'ba Al-Yamaniya or Al-Ka'ba Ash-Shamiya. The Prophet said to me, "Won't you relieve me from Dhu-l-Khalasa?" So I set out with one-hundred-and-fifty riders, and we dismantled it and killed whoever was present there. Then I came to the Prophet and informed him, and he invoked good upon us and Al-Ahmas (tribe) .

Musanif Ibn Abi Shaybah, 6/586, Kitab-ul-Hadood, chapter of في الزنادقة ما حدهم (link):

Some people used to worship their idols secretly. They were arrested and brought to 4th caliph Ali Ibn Abi Talib. He consulted the people how to punish them. People suggested to kill them. Ali said: No, I will not simply kill them, but I will do that act which was performed by them against my ancestor Abraham. After that Ali burnt all of them in the fire.

Disagreement among Muslim Scholars regarding the killing of ALL Polytheists after the death of Muhammad

All Muslim Scholars agree that Muhammad didn't leave any polytheist to survive by paying Jizya. He compelled them either to accept Islam or to be slaughtered. 

Al-Muhalla bi’l-Aathaar:

لم يختلف مسلمان في أن رسول الله - صلى الله عليه وسلم - لم يقبل من الوثنيين من العرب إلا الإسلام أو السيف

There is no difference among the Muslims that the Messenger of Allah ﷺ did not accept anything from the Arab idolators except Islam or the sword

Ikhtilaf al-Fuqaha:

أجمعوا على أن رسول الله - صلى الله عليه وسلم - أبى أخذ الجزية من عبدة الأوثان من العرب ولم يقبل منهم إلا الإسلام أو السيف

There is consensus that the Messenger of Allah ﷺ refused to accept Jizya from the idol worshipers from the Arabs and did not accept anything from them except Islam or the sword

But the disagreement occurred later among the opinions of 4 Sunni Imams: 

• Imam Shafi'i and Imam Ahmed bin Hanbal (and present-day Salafists) all rule that except for Jews/Christians/Magians, all other non-Muslims (like Atheists, Buddhists, Hindus etc.) should be killed all over the world. They don't have any right to stay alive even after paying Jizya. 
• But Imam Abu Hanifa and Imam Malik said that the killing of all other non-Muslims was limited only to the Arab polytheists. But non-Arab polytheists can be allowed to stay alive by paying Jizya. 

ٰIbn Kathir wrote under the commentary of verse 9:29:

وقد استدل بهـذه الآية الكريمة من يرى أنه لا تؤخذ الجزية إلا من أهل الكتاب أو من أشباههم كالمجوس كما صح فيهم الحديث أن رسول الله صلى الله عليه وسلم أخذها من مجوس هجر وهذا مذهب الشافعي وأحمد في المشهور عنه وقال أبو حنيفة رحمه الله: بل تؤخذ من جميع الأعاجم سواء كانوا من أهل الكتاب أو من المشركين ولا تؤخذ من العرب إلا من أهل الكتاب. وقال الإمام مالك: بل يجوز أن تضرب الجزية على جميع الكفار من كتابي ومجوسي ووثني وغير ذلك ولمأخذ هذه المذاهب

This noble verse was cited as evidence by those who believe that the jizya (a tax paid by non-Muslims living in a Muslim-majority state) should only be collected from the People of the Book or from those who are similar to them, such as the Zoroastrians. This is the opinion of Imam al-Shafi'i and Ahmad ibn Hanbal in his most famous opinion.

Abu Hanifa said: "On the contrary, the jizya should be collected from all non-Arabs, whether they are People of the Book or polytheists. However, it should only be collected from Arabs if they are People of the Book."

Imam Malik said: "On the contrary, it is permissible to impose the jizya on all infidels, whether they are People of the Book, Zoroastrians, polytheists, or others."

The Ijma' (Consensus) of the Companions of Muhammad still allows killing all non-Arab non-Muslims

Although Imam Abu Hanifa and Imam Malik gave a ruling that all non-Arab non-Muslims are allowed to stay alive by paying Jizya, but it goes against the direct consensus of the Companions of Muhammad. 

When Umar Ibn Khattab conquered Persia, he used this same verse 9:5 as an argument to kill them, and all the Sahaba (companions) stayed quiet upon it and no one opposed Umar Ibn Khattab by telling him that this verse was limited to Polytheist of Mecca or Arabia only. Therefore, there was an IJMA (unanimous decision) by Sahaba upon this verse that it ordered the killing of all the Polytheists (even if they are non-Arabs).

But then Umar Ibn Khattab didn’t kill the Persians while Ali and 'Abd al-Rahman ibn 'Awf told him that Magians of Persia were also counted as “People of the Book” by Prophet Muhammad. Thus, he took Jazya from them, and then he let them live.

Imam Ibn Hajr al-Asqallani recorded this Sahih (authentic) tradition (link):

وروى عبد بن حميد في تفسير سورة البروج بإسناد صحيح عن ابن أبزى " لما هزم المسلمون أهل فارس قال عمر : اجتمعوا . فقال : إن المجوس ليسوا أهل كتاب فنضع عليهم ، ولا من عبدة الأوثان فنجري عليهم أحكامهم فقال علي : بل هم أهل كتاب "’

When Muslims defeated the Persians, then Umar Ibn Khattab asked Sahaba (companions) to gather and to tell him what to do with the Persians as they are neither from the “People of Book” that they could take Jizya from them, and nor were they the polytheists that they should all be killed. Upon that Ali Ibn Abi Talib told him that Magians were also counted as “People of the Book”.

Thus, the Persians escaped the slaughter while they were also counted as the “People of the Book”, otherwise they would have also been killed as polytheists.

This shows that:

• The order to kill the polytheists was not limited to the era of Muhammad (but this order stays true even after his death).
• And it was also not limited to only Arabia, but all non-Muslims of the whole world have to be killed by Muslims. 

Look at this “authentic” tradition of Sunan Abu Dawud (link):

لم يكن عمر يأخذ الجزية من المجوس حتى شهد عبد الرحمن بن عوف أن رسول الله صلى الله عليه وسلم أخذها من مجوس هجر .

Umar Ibn Khattab didn’t want to take Jizya (but wanted to kill them all), but 'Abd al-Rahman ibn 'Awf told him that Prophet Muhammad took Jizya from the Zoroastrians of the place of Hijr.

Present-day Salafis still consider that all polytheists of the whole world should be killed according to the order of verse 9:5

Saudi Grand Mufti Ibn Baaz wrote (link):

، والأرجح أنه لا يلحق بهم غيرهم ، بل هؤلاء الطوائف الثلاث هم الذين يخيرون ؛ لأن الرسول قاتل الكفار في الجزيرة ولم يقبل منهم إلا الإسلام ،
Translation:
And the correct view is this that polytheists (of today) do not come under the category of “people of the book”, but only Jews, Christians and Zoroastrians are allowed to live by paying Jizya, while Prophet Muhammad killed all the polytheists in Arabia and accepted nothing from them, except Islam.

The largest Salafi Fatwa Website for Muslims, i.e. Islam Question Answers wrote (link):

Other scholars said that this (verse of No compulsion in the religion (Quran 2:256) applied in the beginning, but was subsequently abrogated by Allaah’s command to fight and wage jihad (Quran 9:5). So whoever refuses to enter Islam should be fought when the Muslims are able to fight, until they either enter Islam or pay the jizyah if they are among the people (of book) who may pay jizyah (i.e. Jews/Christian/Zoroastrians). The kuffaar (polytheists) should be compelled to enter Islam if they are not people from whom the jizyah may be taken, because that will lead to their happiness and salvation in this world and in the Hereafter. Other scholars said that this applied in the beginning, but was subsequently abrogated by Allaah’s command to fight and wage jihad. So whoever refuses to enter Islam should be fought when the Muslims are able to fight, until they either enter Islam or pay the jizyah if they are among the people who may pay jizyah.

Obliging a person to adhere to the truth in which is guidance and happiness is better for him than falsehood. Just as a person may be forced to do the duty that he owes to other people even if that is by means of imprisonment or beating, so forcing the kaafirs to believe in Allaah alone and enter into the religion of Islam is more important and more essential, because this will lead to their happiness in this world and in the Hereafter. This applies unless they are People of the Book, i.e., Jews and Christians, or Magians, because Islam says that these three groups may be given the choice: they may enter Islam or they may pay the jizyah and feel themselves subdued. 

Some of the scholars are of the view that others may also be given the choice between Islam and jizyah, but the most correct view is that no others should be given this choice, rather these three groups are the only ones who may be given the choice, because the Prophet (peace and blessings of Allaah be upon him) fought the kuffaar in the Arabian Peninsula and he only accepted their becoming Muslim. And Allaah says (interpretation of the meaning): 

“But if they repent [by rejecting Shirk (polytheism) and accept Islamic Monotheism] and perform As-Salaah (Iqaamat-as-Salaah), and give Zakaah, then leave their way free. Verily, Allaah is Oft-Forgiving, Most Merciful”

[al-Tawbah 9:5]

He did not say, “if they pay the jizyah”. The Jews, Christians and Magians are to be asked to enter Islam; if they refuse then they should be asked to pay the jizyah. If they refuse to pay the jizyah then the Muslims must fight them if they are able to do so. Allaah says (interpretation of the meaning): 

“Fight against those who (1) believe not in Allaah, (2) nor in the Last Day, (3) nor forbid that which has been forbidden by Allaah and His Messenger  (Muhammad), (4) and those who acknowledge not the religion of truth (i.e. Islam) among the people of the Scripture (Jews and Christians), until they pay the Jizyah with willing submission, and feel themselves subdued”

[al-Tawbah 9:29]

And it was proven that the Prophet (peace and blessings of Allaah be upon him) accepted the jizyah from the Magians, but it was not proven that the Prophet (peace and blessings of Allaah be upon him) or his companions (may Allaah be pleased with them) accepted the jizyah from anyone except the three groups mentioned above. 

That is why ISIS allowed the Christians of Iraq to pay Jizya and didn’t kill them. But ISIS didn’t accept any Jizya from the Yazidi community of Iraq, and they killed the Yazidi men and took all their women and children as slaves.

If Shafii, Hanbalis or Salafists of today form an Islamic State/Caliphate today, then again they will start killing all the polytheists and will not accept any Jizya from them. In this regard, there is no difference of opinion between ISIS and the Salafists (and all the followers of Imam Sahafii and Ahmed bin Hanbal). 

Islamic apologists: Verse 9:6 permits to give shelter to Polytheists

Islamic apologists come up with this excuse today that verse 9:5 didn’t order the killing of all the polytheists, while verse 9:6 allows giving shelter to the polytheists too.

Answer:

This excuse is wrong, verse 9:5 is about the polytheists who live within the boundaries of the Islamic State, while verse 9:6 is only about such polytheists who come from the Non-Muslim States (Daar-ul-Kufr), and thus they have not heard the message of Islam earlier. Therefore, if such polytheists want to hear the message of Islam, then they can be given shelter for a short period temporarily. But after that temporary period, those polytheists should either accept Islam, or return to their respective non-Muslim State, and they are not allowed to permanently live in the Islamic State. According to Muslim Scholars, this temporary period could be from 4 months to one year maximum.

(Quran 9:6) If any of the pagans ask you to give them refuge, give them asylum so that they may hear the words of God. Then, return them to their towns for they are ignorant people.

Ibn Kathir writes under the commentary of this verse 9:6 (link):

والغرض أن من قدم من دار الحرب إلى دار الإسلام في أداء رسالة، أو تجارة، أو طلب صلح، أو مهادنة، أو حمل جزية، أو نحو ذلك من الأسباب، وطلب من الإمام أو نائبه أماناً، أعطي أماناً ما دام متردداً في دار الإسلام، وحتى يرجع إلى مأمنه ووطنه، لكن قال العلماء لا يجوز أن يمكن من الإقامة في دار الإسلام سنة، ويجوز أن يمكن من إقامة أربعة أشهر، وفيما بين ذلك فيما زاد على أربعة أشهر، ونقص عن سنة ، قولان عن الإمام الشافعي وغيره من العلماء رحمهم الله.

... those who come from a state of non-Muslims, to the area of Islam, delivering a message, for business transactions, to negotiate a peace treaty, to pay the Jizyah, to offer an end to hostilities, and so forth, and request safe passage from Muslim leaders or their deputies, should be granted safe passage, as long as they remain in Muslim areas, until they go back to their land and sanctuary. Scholars say that such a person should not be allowed to stay in Muslim area more than one year. He could stay for four months to one year, and there is a difference between the sayings of Imam Shafii etc. among the Scholars etc.

The Logic for differentiating between Arab polytheists and non-Arab polytheists is FLAWED

The two Sunni Imams (Abu Hanifa and Malik) later gave a fatwa that killing was limited only to the Arab polytheists. 

But the question arose: Why? What is the logic behind it? 

Islamic apologists present the following logic behind this: 

Arab polytheists had the same Arabic language as the Quran. Thus they were able to understand the MESSAGE clearly. But despite that, when they deny to accept the messages, they deserved to be killed. The non-Arab polytheists didn't get this punishment, while they were not able to understand the message while their language is not Arabic.

Clearly, this logic is flawed and makes no sense, as:

• Even a non-Arabic person can clearly understand the Quran through translation, explanation and interpretation. 
• Many Arab polytheists of the era of Muhammad were illiterates. Many non-Arab educated polytheists excel them in understanding and knowledge of the Quran. 

Therefore, the truth is that this ruling makes no sense. 

It seems Abu Hanifa and Malik were forced to make this new ruling on their own. Islamic caliphate spread to many areas during their era, and there were millions of polytheists (non-Muslim) there, and it was not possible to slaughter them all. 

Perhaps Islam is the most oppressive religion on the planet Earth. Perhaps there never existed any such an oppressive religion which slaughtered millions of people only while they didn't believe in it. 

Conclusion:

• Don't take the danger of Islam lightly. 
• Don't let Islamic apologists fool you by presenting Islam as a harmless religion till the time they are weaker than you.