Kyle, I'd like to meet your children and see how careful you've been not to indoctrinate them with your views on gun control, taxes, sex, politics, alcohol consumption, style of clothing, and yes, even religion. In the real world, kids pick up on the views of the people around them and believe in all kinds of well-founded fact and untenable nonsense while rebelling against a lot of other well-founded fact and untenable nonsense. You are no more going to have a neat, clean sit-down with your child to help him calmly choose his life-path, or whatever, than you are going to keep him free from "indoctrination."
FWIW, I know a guy who was "indoctrinated" by his parents to be quite a sharp, well-read young atheist, who enjoyed debating hapless Christians. In his mid-teens, he was quickly "indoctrinated" by my very conservative church. He's a preacher now. Happens the other way, too.