I believe that religion can be used as a form of brainwashing should a parent or other authority figure choose to use it that way. Belief in God and organized religion are separate things. Religion can be a zealous devotion to anything one chooses. One could decide that cheese is almighty and that in order to appease cheese we should kneel before it and pray three times a day. This could be called religious. If you get several more people to agree that cheese is all powerful and they all do the same thing, then you've got an organized group religion. All they have to do now is write a book and go out and spread the word and you've got yourself a bunch of cheesites.
So yes, religion can be used as a form of brainwashing. Children should be allowed to question what their taught and draw their own conclusions. If they have a calling to faith and religion, fine. If they don't, it should not be cause for punishment or chastising. Otherwise they are adopting religion out of fear and not belief.
Another scenario is that they have been sheltered from the world so that they are not exposed to other ideas. This way they will never know that there are options besides the one presented to them in their home or community. Another common way to control children with religion is to tell them that they will "go to hell" or be "eternally damned" or "won't have everlasting life" if they engage in certain behaviors or ways of thinking.
Most religious adults adopt religion as "the truth". They honestly believe that they are protecting their children by indoctrinating them into a belief system at an early age. They would not call it brainwashing, they would simply call it telling them "the truth", or "showing them reality" because they honestly believe that's the case. However, you have to consider that many adults are brainwashed, or not actively thinking about the choices they make in life, and why they make them. Many people just don't question information, or where the information comes from. They just accept it for what it is.