I think I know why Atheists make people uncomfortable.
1. To the religious or somewhat religious, they are a reflection of just how low you can go, how completely you can abandon the ultimate Good. This is much like how the dead unnerve us. The dead are harmless, but they remind us of our own mortality, and we don’t like to think of ourselves as corpses. Although I wouldn’t say Atheists are necessarily harmless.
2. They are the embodiment of Doubt. Having thoughts that perhaps accounts of Jesus’ miracles were a little exaggerated, or having concerns that God isn’t real, that’s one matter. But seeing a person who is confident that all your doubts are valid…especially if that person doesn’t seem consumed by pain and turmoil like you are when you are in doubt…that can give the religious an ugly feeling that the doubts might have some merit. And then to remain good believers they have to fight this feeling, which to the mind is stressful and tiring. But then, it comes down to the universal divider of men.
3. They are Different. Seeing two men making out might make a person uncomfortable because they were raised seeing a heterosexual couple in every storybook, in every movie, and in every home. To many people, religious or at least quietly nonreligious persons were the world around them. And the fact that some people are not only Atheist, but seemingly happy and well-behaved people while being so, is a challenge of expectations. And a challenge to someone’s norm will make anyone uncomfortable. Like me is safe. Different from me is dangerous. Atheists are going to hell, and at best, are sadly mistaken.