Lewis Wells at Commandments of Men shows the difference between teaching and indoctrination, and shows how he sees it fleshing itself out in the environment of patriarchy. Read his post here. Although he specifically ties this difference to patriarchy, the definitions fit for almost any type of belief system. Aberrant views can be indoctrinated, but truthful ones can be as well. One can be a mindless fundamentalist with the truth.
Wells explains that proper teaching leads one to have one's own moral compass, and gives one the ability to discern. A good compass in determining whether instruction is one or the other is in how those that do the teaching deal with the conclusions of the taught. If they are open to differing viewpoints of those they teach, there is a greater likelihood that they truly wanted to teach rather than indoctrinate. I've had numerous situations in my Christian experience where I've come to different conclusions than those that taught me. Their reactions to my ideas have been fairly telltale as to what kind of teachers they were.
Good teaching also helps to avoid being intimidated by teachers who think they know the truth in an absolute sense. One thing I've noticed about teaching is that the humility level of the teacher is quite contagious.
Let not many of you become teachers, my brethren, knowing that as such we will incur a stricter judgment. James 3:1