I'm having the exact same problem! I've been an atheist since fifth grade -- I'm a high school sophomore now -- and it scares me to death to even consider coming out.
I had an unfortunate experience with it in seventh grade. My classmates were talking about nothing in particular, and somehow the conversation shifted to religion. Someone asked me if I believed in God, and I replied, unabashedly, "No." They were all shocked! One girl actually said that she couldn't be my friend if I was an atheist. She asked me a couple of questions, like "Where do you think you came from?" to which I replied, "My parents." Duh, right? Then she asked where my parents -- no, people in general -- came from. I didn't know as much as I do now, so I had a bit of trouble answering that one.
But that experience taught me something: never make that mistake again. And so I have lived ever since. I either tell them I believe, or that I'm an agnostic. Lately I've been telling them the latter. I always see to it that I stay in the closet, because I don't know how people will react. Some hypervigilant part of me always anticipates a bad reaction -- and for me, bad reactions equal hits on my self-esteem.
It's a real drag keeping this a secret. I've been bullied for eight years, though, and I want to escape that, not walk right back into it! I know this next part sounds really stupid, but -- how else will I be happy?