This is something I also struggled with. I have two children: a son, now 14, and a daughter, who'll be 8 at the end of the month.
I had custody of my son for the first four years of his life, after which his mother begged me to let her take him back. She actually enrolled him in a private Christian school which he attended for several years. I avoided the subject of religion around him, preferring to just enjoy his company whenever I could see him, but if he had asked I had resolved to always be honest with him. Last year I was surprised when he told me had decided Christianity was not for him, and he hadn't been a believer for a long time. Some things just work out like that. I'm sure this will sound odd to believers, but I was so proud of my boy on that day.
My daughter, however... I tried to instill in her a tolerance for all faiths, and decided I'd answer any questions she had as best, and as honestly, as I could. It was important to me not to "force" any kind of religious beliefs on her, but rather give her as much information as possible so that she could make an informed decision for herself. Unfortunately, a family tragedy sent my daughter to live with close family, who, although kind and well-meaning, presented Christianity to her as the absolute, indisputable truth. They also sent her to questionable churches, the kind she comes back from and says things to me like, "Daddy, please believe in Jesus! I don't want you to burn in hell forever!"
Needless to say, I was not then, and am not now, amused to hear my then-5-year-old little girl saying these things. So I tell myself as she grows, she'll see things differently. I do my best to respect her beliefs, and not try and change her mind, or argue with her (though for a while, her favorite thing to do was try and provoke a faith-based argument); I tell her, "Look, sweetie, I don't disrespect your beliefs, or try to convince you they're wrong, you need to show the same respect to me."
I was very, very worried about my children being indoctrinated into Christianity, but then I remembered something... I was brought into the church as very young, naïve, impressionable child, and I managed to see through it all, and find my way out. My son has, too. So I nurse the hope that one day my daughter will either wake up and see something that changes her mind; or at the very least that I'm able to better teach her about tolerance, and respecting the beliefs of others. I feel like the world would be a much better place if tolerance (religious and otherwise) was more widespread, or a priority at all for most people.