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It's painful and lonely, but it's normal, and it will most likely pass. I grew up in a similar household, and when I was in high school I started to have questions: why should only Christians go to heaven? why, when all my bunkmates at church camp felt driven to go down to the altar at the end of the service, didn't I feel the same compulsion? why was preserving sexual purity more important than alleviating poverty? And on and on and on. It only got worse in college, when I met *gasp* gay people for the first time and realized they were impossible to distinguish from everyone else, they were nice, and some of them attended my liberal Protestant church. Oh, and then I fell in love with an atheist and ended up marrying him.
All this really, really bothered my mother, especially the atheist son-in-law part. Drove her to tears and mad, raving screeds sent to me in the mail. And it was upsetting to me. I loved my parents, and yet what I was learning--all my new beliefs and values that made perfect sense to me--was driving a wedge between us. There were arguments and silences and long, tense, polite superficial conversations. And yet--
And yet, somehow, we got through it, and the realization that life is short and people who love you are priceless made it possible for these things to no longer matter. Now, when I see Mom or talk on the phone with her and one of these things comes up, one or the other of us will say, "You know how I feel about this stuff," and we let it drop and go on to a much more mutually satisfactory topic of conversation, like Mom's crazy neighbor's daughter's disastrous marriage, or loony Mike Huckabee (Can you BELIEVE that guy? Oh, yes, my mother's a Democrat *and* an evangelical.)
This distancing--it's going to happen. It's got to. It's part of growing up. For you, it might turn out to be surprisingly mild and relatively painless. Maybe your parents will amaze you by being much more tolerant of differing views than you imagined, because everything else about you will turn out just fine. Or maybe they'll react even more violently than my mother did. I'd be remiss not to caution that there's a slight chance that you'll always feel alienated, that they'll never accept your difference, but I think that's not all that likely.
Not to proselytize, but you really sound like you might be a Unitarian-Universalist unawares. When you get to college, check out your local UU congregation or fellowship and see if you fit there. Or, as another letter-writer suggests, try some liberal Christian congregations, like the UCC, the Quakers, some Episcopalian parishes...there are even socially progressive RC churches, if you're of that persuasion. Whatever you do, find a multigenerational congregation. It was comforting to me to have older folks whom I could look up to, while things weren't completely sympatico with my mother. Because you know, then, that other people question and doubt, too, and it's reassuring to know that they turned out just fine.