Our religious differences were a big problem a few years ago when we had two kids and I found out that her church was a young-earth-science-is-evil-the-Bible-is-infallible fundamentalist church. (Her description of it as "a basic Bible-believing church" had not done it justice at all.) Eventually I started attending a Unitarian-Universalist church and bringing the kids so they would get an alternative viewpoint (her service started at 9:30 and mine at 11:00 so they attended both each week). Recently my wife switched to a socially and theologically liberal Methodist church because she has evolved away from her fundamentalist views, so it's not nearly as much of an issue. BTW, most UU churches are atheist-friendly, and I have found it to be nice way to connect with a like-minded community and deepen my non-theist spirituality (which sounds like an oxymoron to most people, but it's not). I'd probably have a similar experience with my local Humanist group, but I'd have another big fight on my hands. She accepts the kids attending UU services because it's a church.