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 of killing Polytheist has become a problem for Islam apologists, while the writer of 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.

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

Therefore, Zakir Naik tried to deceive people and claimed in this video:

  • Verse 9:5 of Quran ordered to kill “only” those polytheists, who made a treaty with Muhammad, but later they violated that treaty.
  • And 2nd lie that Zakir Naik is telling is this that these polytheists could also be only killed when they came to the battlefield and start a war.

Contrary to these lies of Zakir Naik:

  • The peace treaty which Muhammad signed in 7th Hijri year (at time of victory of Mecca) was not with whole of Arabia, but only with the tribes living in Mecca and around it.
  • In 9th Hijri year, Muhammad got “absolute power” and no one was left there in whole Arabia who could have opposed him. Thus, then in 9th Hijri year, Muhammad claimed the revelation of the verse 9:5 and made killing of all polytheists Halal (permissible) for Muslims.

Therefore, even if we have to accept that some tribes of Mecca and around violated the peace treaty, still question is this why Muhammad made permissible the blood of polytheists of whole Arabia through this verse?

And this is also a lie by Zakir Naik that this verse orders to kill only those polytheists who are fighting against Muslims in a battlefield. Quran is very clear that after the 4 months, “all” the polytheists had to be killed, without any difference of them being peaceful or at fight with Muslims.

And the Quranic verse 9:29 again testifies the same thing that order of killing of all polytheists 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.

(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.

Note: This verse also allows Jizya from only the “People of Book” (i.e. Jews and Christians and Zoroastrians), while polytheists were not even allowed to live after paying the Jizya.

And then there are traditions which are clear 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.

And 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 orders killing of all the Polytheists.

But then Umar Ibn Khattab didn’t kill the Persians while Ali and 'Abd al-Rahman ibn 'Awf told him that Zoroastrians of Persia were also counted as “People of Book” by Prophet Muhammad, and 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 "’
Translation:
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 Zoroastrians 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 order of killing the polytheists was neither limited to the era of Muhammad (but this order stays true even after his death), nor it was limited to only Arabia, but for whole world. And it was also not limited to the battlefield, while Persians had already been defeated and they had already surrendered, but still Umar Ibn Khattab wanted to kill them all had they not accepted Islam. 

And now 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 .
Translation:
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.

Imam Shafii, Imam Ahmed bin Hanbal, Imam Ibn Hazam all said that all polytheists of whole world should be killed according to this verse 9:5, and no Jizya can be taken from them, and they have only one choice to save their life i.e. to accept Islam.

While Abu Hanifa limited this order only to the polytheists of Arab, but non-Arab polytheists could pay Jizya and stay alive according to him. Nevertheless, Abu Hanifa went against the Ijm'a of Sahaba, where Umar Ibn Khattab wanted to kill the non-Arab Persians due to this verse, and all Sahaba agreed with him (but Persians escaped this genocide while it was proved that they were also from the People of the Book). 

Thus, Imam Shafii and Imam Ahmed bin Hanbal rejected the opinion of Abu Hanfia, by using the Ijma (unanimous decision) of Sahaba, where none of them rejected the opinion of Umar that all polytheists should be killed.

Shafii and Hanbali Scholars used the decision of Umar Ibn Khattab that only the “people of the Book” are allowed to live after paying Jizya. Umar was in doubt if Zoroastrians of Persian were included in “people of book” or not. Thus, had it been proved upon him that they were not from the “people of the book”, then he would have compelled them to accept Islam like the polytheists, and if they had rejected to accept Islam, then he would have killed them all.
References:
(1) Imam Shafii, Kitab al-Am, vol. 4, page 174
(2) Ibn Qadammah Hanbali, Book al-Mughani, vol. 9, page 173

PS: 
The Muslim Sultans who conquered India, took Jizya from Hindus too and didn't kill them. It was due to the reason that they were the followers of Hanafi Fiqh, and Imam Abu Hanifa allowed to take Jizya from the non-Arab polytheists. This saved the Hindus from being slaughtered. 

Present day Salafis still consider that all polytheists of whole world should be killed according to the order of this 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 Fatwa Website of 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 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). 

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

Islam apologists come up with this excuse today that verse 9:5 didn’t order to kill all the polytheists, while verse 9:6 allows to give shelter to the polytheists too.

Answer:

This excuse is wrong, while verse 9:5 is about the polytheists who live within the boundaries of Islamic Sate, 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 of time temporarily. But after that temporary period, those polytheists should either accept Islam, or to 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.

Translation:

... 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.

Conclusion:

Don't take the danger of Islam lightly. 

Don't let Islam apologists fool you by presenting Islam as harmless till the time they are weaker than you.