I think yaarrrggg is half right. It is acceptable to discriminate against atheists. But it's also acceptable to discriminate against Christians. Certain things are OK and others are not. Here's my brief quick list of how I think it goes in the national media (there would certainly be some regional differences). White list is the things you're allowed to discriminate against. Black list is the things you absolutely aren't allowed to discriminate against. There's lots that are gray.

White list
Atheism
Christianity
White people
Southern people
Smokers
Men

Black list
Black people
Muslims
Women
Hispanics