Brainwashed and indoctrinated are over used discriptions that rarely fit what they are describing. When someone says so and so is brainwashed or those people are indoctrinated, it's about dismissing them more then anything else.
Kindergarten through 12th grade is indoctrination. College too. In fact any kind of systematic education should be considered just as much indoctrination as being taught from your parents or from your church. The difference between a good education and indoctrination is the slant that a person views the information being taught. It is an over used term that only shows bias.
Brainwashing is more then just a negitive slant of education. This is the kind of thing that I would count as forced reprogramming of a person. I've heard stories of POWs taken by an enemy that then go through a means to turn that person against their own country. Arguably this could also be catogoritized as what the military does to their own people through boot camp and after. Strip them down of anything they were before and mold them to what the military wants them to be. Even the most positive use of reprogramming a person from a psychologist or a consoler giving cognitive behavior theory to help a patient stop some unhelpful thinking patterns or stop a negitive habit, would fit the catogary of brainwashing, because the therapy is about forcing a patterned thought or behavior to no longer be there.
Yet the way people use the term brainwashing is only applied to religous beliefs (and occasionally political views) that they do not agree with. The term brainwashed (like indoctrination) is used excessively towards the things the speaker does not believe and disagrees with. It's over used and an excuse to hold a negitive opinion due to their already held bias.
I can't speak for you and your beliefs, but I know that I was not indoctrinated or brainwashed. I actually looked into the matter to find out and consider what's true and what isn't. Our culture has so much doubt feeding it from pro-atheistic and anti-Christian philosophy that I would argue that most people consider if their beliefs are reliable or not. This dynamic alone should shut down the perspective of rampant indoctrination and brainwashing. But unfortunately that would also mean that those terms and perspectives against religion (and against Christianity specifically) are invalid and don't have a leg to stand on.
I'll get off my soap box now but brainwashing is one of the terms that I get angry about.