The reason it would seem makes a certain amount of sense when you understand that the general trust members of a large society extend to strangers is due to a shared fiction that makes it possible to know generally what to expect from someone when you don't know them personally. "Oh he's a Christian, so we share a certain value system, and he will likely be bound by the same principles I hold, even though I don't know them personally." These shared fictions, these narrative structures serve as a means to extend trust beyond the few you actually have the opportunity to develop a direct relationship with. It's the same thing with money. That is a shared fiction with inherent value built right into it that allows strangers to relate to each other on a common ground.
So, when those who participate within a given shared fiction encounter someone they perceive as directly rejecting that shared fiction, what bridge is there with other strangers, is missing with this stranger. It's different that the normal suspicion with those from other cultures as well, since it is recognized they have their own shared fictions, belief systems, that bind and hold them together in generally moral and respectful ways. With the atheist, that is someone of their own culture who denies validity to their shared fiction, alienating themselves from their cultural brothers and sisters, like say "I'm not like you and don't value what you do". Of course logically, we can see we do have common values with the atheists of our culture, but that level of thinking is a bit more sophisticated than simply operating within the fiction, letting it define truth and reality and society for you. It's a gut level response because the system is thrown out of balance for them. Only a rational level which requires a greater level of sophistication can counter it, in other words. Rationality operates at a much higher energy level, which most people don't use if the shortcuts work for them.