They wish you would disbelieve as they disbelieved so you would be alike. So do not take from among them allies until they emigrate for the cause of Allah. But if they turn away, then seize them and kill them wherever you find them and take not from among them any ally or helper. – Quran 4:89
The above verse is used and manipulated by critics to show that Muslims are allowed to wage war against disbelievers. However, reading the verse that proceeds after, verse 4:90, states the following,
4:90 Except for those who take refuge with a people between yourselves and whom is a treaty or those who come to you, their hearts strained at [the prospect of] fighting you or fighting their own people. And if Allah had willed, He could have given them power over you, and they would have fought you. So if they remove themselves from you and do not fight you and offer you peace, then Allah has not made for you a cause [for fighting] against them.
It is evident reading the verse in its contextual context that the passage does not encourage indiscriminate violence against disbelievers, just because of their faith. Verse 4:90 tells Muslims that if the disbelievers moved away and ceased hostilities against the Muslims, that they, the disbelievers be left alone.
The Holy Quran Arabic Text with English Translation, Commentary and comprehensive Introduction – Maulana Muhammad Ali
88a. Clearly those waverers are implied here who went back to disbelief after they accepted Islåm, and thus again joined the disbelievers. As to their identity, there are six different conjectures, and I need not puzzle the reader with these.
90a. This verse explains the previous one, showing clearly that even waverers were not to be killed or fought against if they refrained from fighting, though they may have gone over to disbelief after accepting Islåm. The commentators agree that the persons referred to in this verse were disbelievers and not Muslims, and they are generally supposed to have been the Banß Mudlaj (Bd). Note also that we have here the clear injunction that if any people offered peace, they were not to be fought against. 
 The Holy Quran Arabic Text with English Translation, Commentary and comprehensive Introduction [Year 2002 Edition] by Maulana Muhammad Ali page 221 – 222