To be fair, I don't think they're saying Jason was born bad. On the contrary, he was born good but is currently screwed up due to trauma that Bruce did nothing to heal. I think it's saying that he *can* change, he just needs to deal with that stuff.
Not that Jason isn't getting the short end of the stick (and Bruce's "Dear Jason, sorry you fail so much! is just...oh, Bruce)--he had a worse childhood and winds up being "the bad one." But given everything Jason's been through it's hard for me to really point to his dad being a criminal as the source of his crazy.