I love this discussion, because it brings up things I'd not thought of. I think that John suffers from such a narrow focus that he can't understand, fundamentally (at least in this universe, and who knows how many others) that while Dean can hear an order snapped out and follow it (yes sir, no sir, no excuse sir) without a loss of self (in the ordinary sense, not to go into the whole Dean self worth discussion), whereas Sam is so much like John that a short explanation would have done worlds of good getting Sam to following in line. But the explanation never came, and hence, John has trouble with Sam. And Sam won't give in. And the conflict often, I think, spirals out of control.