Woa geeze, some of these posts suprise me.
I must say I'v never thought there would be such problems with such a thing, and Im fairly casual about affirming that im an antheist (couldnt relate it to the idea of 'comming out of the closet' at all.) And I can't actualy remember when I switched to being 'unsure' and then to definatly being an atheist. However, my parents werent even regular church goers.
But if it's any consolation, Iv gone to a catholic school all my life, and had no problems.
Of course, I gradualy progressed toward atheism as I actualy learned more about the nature of reality, so you might want to consider starting off with something like "I'm not sure i actualy beleive in god" Raise some question or another and test them; see how they bite, if they explode, well then, might want to indeed keep it a secret for now.
But if they dont react too badly, just lead them on slowly, maby over the course of a month or three w/e.
On the other hand, you could take the sympathetic route: Cry, and when asked what's wrong, say something like "Iv been too scared to tell you but..." etc... You know, something cheesy like that
Use empathy to your advantage.
-Andrew