I think most people find the most important being in life is God and knowledge of him is a foundation of our existence. Most people also feel they just know God exists but don't know how. When you have people not believing in God, to many believers, it feels like they are committing a huge crime. They feel a core aspect of being a good human is to believe in God, or even know he exists. Although people of different religions see each other in wrong, and Christians condemn people of other faiths, the foundation of their faith, is belief in God, and they feel at least other people of other faiths have accepted that. They tend to feel more hostile towards them, because, they are disregarding the core of their spirituality. Without God, what is the spirituality of a human?
Of course intolerance is not justified, but it comes from these sort of feelings I suspect.
Of course intolerance is not justified, but it comes from these sort of feelings I suspect.