It’s always a tough issue deciding how to deal with raising a child as a skeptic/atheist/agnostic in a predominantly religious community. My daughter will be entering 1st grade in the Fall, and though we live in a fairly varied and progressive community, even here Christianity is the most visible and dominant point of view. It’s tough to stand out, and even tougher on the kids. I conspicuously leave out “under God” when reciting the pledge of alliegiance in my daughter’s classroom, but in our community no one’s likely to give her or me a hard time about it. It sounds like you’re not so lucky in your community, and that makes your choices tough. I do absolutley agree that the influence of school, teachers, and especially peers becomes important especially in later grade school, and it’s understandable to be worried about how that wil undo your efforts at home.
On the other hand, as a skeptic and freethinker, I am wary of homeschooling for primarily ideological reasons. My brother-in-law home schools all his kids because as an evangelical Christian he’s terrified they might be exposed to ideas other than his own and be tempted to think for themselves. I think we as freethinkers have to accept that our job is not to insulate our kids from other ideas but to immunize them as well as possible with good critical thinking skills. No one can decide what the right choice is for your kids but you, but I’d be tempted to recommend continuing to present all religions as interesting sets of stories (there are some great mythology bedtime storybooks out there, and I sprinkle in Christian myths as well to make them just one of the pack), to talk honestly about your beliefs but not denying that good, smart people can believe very different, and strange, things, and to do the best you can to teach them to think for themselves and question everything, even if that inevitably means they will question you and your ideas and may come to think very differently.
FWIW, my daughter went to a Jewish Community Ctr. preschool for 3 years and can still recite her Shabbat prayers when called upon to, but we’ve had simple and brief yet very frank discussions about why I don’t believe the same things as some of her teachers and friends’ parents. Sometimes she says “I believe in God because somebody had to make the world.” Other times she says “I don’t believe there’s a god” partly because she wants to be like me. And sometimes she shows the kind of great thoughfulness I hope for when she says “It doesn’t make sense that God would make everybody and love everybody and then kill all the babies [from the Passover story].” I hope she turns out to share my ideas about relgion, politics, etc, and I do admit to stacking the deck as best I can. But I still see my job as teacher her to make up her own mind, and that means she has to be exposed to some of the alternatives to what I think. I hope things work out for you and your kids.