Yeah, I think the word has a very negative connotation.

Ideally, teaching should not so much focused on particular beliefs, but should be focused on giving a person a set of tools to find out their own answers, or to create better ways of thinking. Disagreement should be encouraged ... and even "correct" answer should be counted as partly wrong if there's no reasoning to support that conclusion.

But if a student is presented information and taught not to question what they are taught, it is indoctrination. In this case the teacher's goal isn't really to teach, but to clone their own mind.