When Muhammad invented his new religion he had to contend with a lot of different religions — like Judaism, Christianity, Zoroastrianism, and even many people with no religion at all. So what do we do with all of these people who refuse to follow Muhammad? The Quran is not the best place to find the answer.
In Surat Al-Kahf 18:29 Allah says to be patient with them. Leave them alone. The expanded verse in the link tells us why: Allah has prepared a pit of fire for them. In other words, it is for Allah alone to punish the non-believers. Humans are merely told to ignore them.
But then in Surat An-Nisā’ 4:89 Allah says kill non-believers. What is striking about this verse is Allah wants non-believers attacked from behind. Sucker punch. And when you’re done killing that guy, kill every non-believer you find!
Many would argue — and have, ad nauseum — that this only applies to atheists (well, that’s a relief). But no. It actually applies to all non-Muslims. Christians and Jews are constantly lumped together with atheists in the Quran. I’ve written about this before (literally, about 60% of the Quran is nothing but threats against non-Muslims).
To be fair, I’ve never, ever met a Muslim who condoned violence against atheists or other non-Muslims. I’ve even discussed my atheism over tea with a young member of Hezbollah, and I received nothing but kind words and warm wishes. That’s just the point though. The vast majority of Muslims already eschew the many verses calling for death to non-Muslims. It might be about time that they threw the rest of the Quran into the garbage as well.