However, if we take the position that NOT having a belief in the supernatural / God/gods is by default atheism at birth, then the argument might be made that the parents are indeed indoctrinating, inducing, forcing abandonment of lack of belief (aka atheism) for a preferred supernatural religious belief.
I'd proffer that unless a child is presented with the alternatives to the parents’ preferred religious belief; provided with a variety of options including the option of no belief ... and have it presented dispassionately without prejudice, threat, fear or undue influence, then indeed parental indoctrination of a child into their preferred belief system IS brainwashing.
It is every much brainwashing as a Palestinian child being indoctrinated by his parents to hate and want to kill Jews. Whether it is a mindset of good or evil is in the eye of the believer; it doesn't change the fact that it is inducing a belief, a view, that otherwise might not have been the child's own given the various options.
Some how theists just aren't comfortable allowing their child the "free will" to investigate and decide without coercsion. It's the parents’ will or else. If that’s not brainwashing I don’t know what is.