Most of the critics of Islam and some sites which are promoting false propaganda against Islam quote the Verse

Kill the Mushrikoon (polytheists) where ever you find them , The Holy Qur'an, Chapter 9, Verse 5

to show that Qur'an Commands the killing of Disbelievers

This is quotation taken completely out of context. If you read the chapter(Surah At-Taubah) from the beginning the first verse talks about the treaty between the Muslims and the Mushriks (Pagans) of Mecca.

Freedom from obligation (is proclaimed) from Allah and His messenger toward those of the idolaters with whom ye made a treaty , The Holy Qur'an, Chapter 9, Verse 1

In the next verse The Meccans are given four months time to set things right otherwise a declaration of War and coming to verse [9:5], the complete verse is

But when the forbidden months are past, then fight and slay the Pagans wherever ye find them, and seize them, beleaguer them, and lie in wait for them in every stratagem (of war); but if they repent, and establish regular prayers and practice regular charity, then open the way for them: for Allah is oft-forgiving, Most merciful." The Holy Qur'an, Chapter 9, Verse 5

Hence if you read this in context we know that this statement was made in the battle field. Critics often fail to quote with context. Infact in the battle the Qur'an Commands that a person who seeks asylum should be escorted to a place of security.

If one amongst the pagans ask thee for asylum, grant it to him, so that he may hear the word of Allah; and then escort him to where he can be secure that is because they are men without knowledge." The Holy Qur'an, Chapter 9, Verse 6

The Qur'an explicitly forbids killing

Whosoever kills a human being for other than Murder or Creating Mischief in the Land, it is as if he had killed the whole of Human Kind and whoso saved the life of one as if he has saved the life of all Mankind The Holy Qur'an, Chapter 5, Verse 12