I think one of the issues is the fact that in places where religion is important, people can't even understand that you are not a believer. Even if they try. Even if they have nothing against you. It's not necessarily that they don't want you to have another way to think than them per se, but rather that they can't fathom it. So they may take it as provocation.
I grew up in a very secular country, so until I left I never had this problem: whatever believers thought of atheists, they certainly knew they exist and how they function.
Then I went to Canada and little after, met my Hindu in laws. A whole new experience...
Regarding in-laws, they were happy I was an atheist because of the behaviors of some Christians in India (aggressive proselytism is a understandable worry). But.. actually they understand atheist as 'not very strong believer'. My mother in law in particular, can't get it at all. That's not a worry, and they are great in-laws, so I don't mind. But it remains very weird to me.
And Canada.. well, my first evening here, at a B&B. Saturday evening. Lady of the B&B comes to me, asks me what Christian denomination I am, to direct me to the right church in the morning. Er.. She sees I'm embarrassed. Gives me the address of the synagogue. Sees I'm remaining very embarrassed and that I try to speak, but by the time I did, she was gone and came back with a list of all the possible religions and obscure sects' buildings in the city. Took me ten minutes to make her understand I was not going to need any of that, and she still did not really believe me. At the end she said something that it was okay if I was not very often going to church, that it may change later on, or something like that. Ghhhaa!! Then I had a few embarrassing conversations with customers on the same subject, including one who bluntly told me that not believing was impossible and that I was just doing provocation. Okay??? At the same time, they are a lot of atheist Canadians, even in my region, so I don't know, maybe I don't say things the right way, or maybe some people are just liking to fight over it.. I mean, it's obviously not ME bringing up religious topics with my customers...don't know.. But for sure I get a great feeling of impossibility to simply understand the concept of atheism.