I agree with your point. I consider myself a Christian (and a pretty conservative one, at that), but people look at me like I'm crazy when I tell them I don't think we should "put prayer back in [public] schools". If students want to get together with one another and have a Bible study or prayer time on their own, then that is fantastic. But I don't think public schools should be leading school-wide prayer. A lot of my fellow Christians will get up in arms about it, but what happens if that school principal or teacher leading prayer is muslim, or hindu, or buddhist, or [insert other religion here]? If you set a legal precedent allowing school-sanctioned Christian prayer, you may not like what you get.

Religion should be left to the church and home. If you want your kids' education to include Christianity, then you should look into a private Christian school. But the public school system shouldn't be involved with it.