and that his anger with John isn't so much because of his absences and his lack as a father, but for the ways John actually tried to protect him.

I think that's true, and it's a testament to the fact that John did protect him against all odds.

I mean, it would be natural for Sam to hate the father who let him get hurt, or who made him do horrible stuff. But that doesn't seem to have happened. What comes out when he's angry with John is nearly always the stuff that John did right...but Sam doesn't see it that way.