Why does the Quran say that infidels should be killed?
And when the forbidden months have passed, kill the idolaters wherever you find them and take them prisoners, and beleaguer them, and lie in wait for them at every place of ambush. But if they repent and observe Prayer and pay the Zakat, then leave their way free. Surely, Allah is Most Forgiving, Merciful.
This verse, chapter 9 verse 5, is often used as evidence that Islam allows killing of non-Muslims, but what is not recognized is the context and history behind these verses. The history of this verse is that when Prophet Muhammad(sa) began preaching the unity of God he was persecuted for 13 years, much as Prophets Abraham and Jesus were. Since Muslims who are being persecuted are encouraged to leave for safer areas, rather than create disorder, Muhammad(sa) and his followers migrated to Medina. After they left, the Meccans attacked them in Medina on and off for a period of nine years until Chapter 9 was revealed.
Looking at the context of the verses, it becomes obvious that the commandment of this verse only relates to those tribes who continued hostilities against the Muslims even after they had migrated. In particular, reference is made to 5 tribes (Banu Khuza’ah, Banu Mudlij, Banu Bakr, Banu Damrah, and Banu Sulaiim) that did not honor the treaties they made with Muslims. It is also important to remember that the preceding verses give these people respite for 4 months to reconsider their behavior and cease hostilities. Sadly after 4 months passed, the enemies of Islam continued their hostilities against the Muslims. Only then was Prophet Muhammad(sa)commanded by God to meet them in battle to defend Muslims and the religion of Islam.
Even in this situation the Quran states that if the enemies repent of their behavior and promise to fulfill their treaties, it becomes incumbent on Muslims to cease military action and forgive them. Unfortunately those who take this specific verse out of context fail to see that as the title of the Chapter Al-Taubah suggests, the main subject matter of the chapter is forgiveness and repentance.