Only my Wife and a couple of very close friends know about me. My main reason was initially that my family lives in other states and even though they deserve to know (because it is important to me) it would be best (or most respectful?) to tell them in person. Now however I'm not sure I'll ever tell them because of my daughter. My biggest complaint with the way I was raised is that I didn't have the option to make up my own mind, and I don't want to take that away from her. If she converts later on in her life that's perfectly alright with me, but I don't want her to be forcefully exposed like I was. It took me 24 years to finally figure it out for myself.
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.