I think you're doing a lot of projecting here. I'm not in any way suggesting that anybody is treated as the enemy. I’m not even beginning to suggest that your son owes anybody an apology. And I’m certainly not making any “biased presuppositions” about him. I know you're on Medium, and I know that "White people are awful" articles are the norm. But actually read what I'm saying. I don't hold any animosity towards white people at all. I'd make exactly the same argument in favour of any group who had been though slavery and Jim Crow.
Things like affirmative action and diversity programmes advantage a tiny percentage of black people and disadvantage a tiny percentage of white people. White people will never go through a fraction of what black people went through (nor should they), so no, I don't think they'll grow up feeling "pissed off and ready to tear everything down". Most white people, and especially most young white people, already understand why things like diversity programmes are important.
Lastly, if you think affirmative action is "repeating the same mistakes" as slavery and Jim Crow, you might want to take a closer look at what happened back then. There’s simply no comparing the two. Also, Jim Crow and slavery weren't “mistakes”. They were very deliberate. Bear in mind that Jim Crow isn't ancient history. It was less than 60 years ago. Maybe you think that past injustices should just be ignored, but many people, quite rightly, don't.