I don't think that parents raise them to be gender non-conforming, but more that they accept that the child they have happens to be non-conforming to gender stereotypes, and get on with life with their perfectly normal child.
To force something upon a child - be it forcing them to conform to the societal gender stereotypes, or forcing them not to conform - usually does not go over well. I remember hating it when I was MADE to wear a dress (a uniform I didn't have an issue with, it was in my own clothes that I had an issue being forced to wear dresses), and I'm reasonably (aside from the dress/skirt issue) gender-conforming.
The Jolie-Pitt's accept John/Shiloh (Shiloh prefers to be called "John" I read somewhere) and their choice of clothing, and lack of gender conformity, as normal for their child. They accept it, embrace it and move on - it's never ever been forced on Shiloh/John.
Gender non-conforming is also different to these children identifying as transgender.
I think that a parent realising that their child needs their support isn't likely to be a bad thing. It's the support or lack thereof that could cause the problem.