I suggest someone fearful of retaliation, at least from their family, take it slow and pretend to be slowly losing faith. This will backfire if you are under 18 and your parents are the kind to force you to horrible camps, workshops, etc if they think it will force the faith back in. But start with saying things like "I'm questioning the bible/God/our religion" or "I disagree with what the pastor said" or bring up one of the issues in religion you know well that turned you atheist, and express it as a problem to them. Later express your disgust or shame of the worst people in your parents' religion and make it clear you have a problem with being associated with them. Take it as slow as you want, you can progress to then being a deist or an agnostic and once they get used to that start with atheism. Or maybe you'll find that you won't even need to come out as an atheist if coming out as an agnostic stopped them from talking to you about religion. The point is they will learn a little bit about other perspectives if you give them time to reflect at each of your stages. You can change their tolerance of others' beliefs this way.
My parents are pseudo-christian cult members and after about a year they accepted my atheism.
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?