My biggest one is that because I "don't believe in anything" that means my view doesn't have to be respected. I've come across maybe two people in my life who displayed this behavior towards me in person, but it was enough to get my blood boiling. Also, these are people who won't tolerate any criticism towards their religion, friendly or otherwise. They expect people to revere their opinion as much as they do and tip-toe around their feelings. That's another thing I can't stand. The blatant hypocrisy.
I personally don't mind the stereotypes, people will always use familiar terminology so I don't really blame them for that. What does annoy me is the response that since science does not know how the universe began, it must have been god. That one does become tiresome.