You can understand where it comes from. In the bible belt especially, the few examples you get of atheism are just bad. You're raised to think only evil, awful people even consider it.
I mean look at it, people who have lost faith in the church, and question the teachings, don't really believe in a god anymore, how many of them will refuse to call themselves atheists, even though that's exactly what they are?
Hell, this website does the same thing. They say agnostic, and that's fine, except it isn't really for true agnostics. You can be unsure and still believe, those people are agnostic believers. The first sentence in the "about us" section of this website says "Agnostic.com is a non-profit and non-prophet community for people who are naturally good without any gods."
That's not agnostic. That's atheism. Agnostic atheism, sure, but still atheism.
So yeah, it's a problem. We don't do a lot to dispel it, but there isn't really an atheist "movement" to educate people because atheism isn't really a belief system so what can ya do?