The determining factor on whether a teaching method can be thought of as indoctrination is simply how you handle their questions and doubts.
Parents who indoctrinate their children stifle questions. This can be done in many ways: through abuse (physical or otherwise), or simply by saying that such a question is not proper to ask. Basically, anything to avoid answering the question.
On a lower level, which is I suppose on the fringe and may or may not be considered indoctrination, is when parents give a dishonest answer where they twist the facts or outright lie.
My situation is quite different than normal indoctrination because I lost my faith almost right when I became a legal adult. I can't recall, off the top of my head, how my parents handled questions from me when I was a believer.
I talked with my parents a lot during my exploratory phase as a brand new atheist and they took their own angle: they didn't lie, but they gave very poor, dissatisfying answers that almost always raised even more questions. When I pursued the line of reasoning, they would then shut me down and say something like, "We answered your question. All you want to do is argue." I still do discuss religion with them, although they generally don't want to discuss it back and I have to kind of wrestle it out of them. Normally it would be wrong to coerce people into discussing religion when they don't want to, but I consider my parents to be a special exception since they are the ones who put all these ideas into my head in the first place.
So to answer your question, 2PV (and I do like to answer questions, seeing as how I'm against indoctrination
), I need to ask a question back at you: how do you handle their questions? If your children were to hurl one of the many cripplers of Christianity at you, how would you respond?