It's perfectly fair to dislike John for the things he did wrong. He certainly screwed up those boys. For me...well, I understand where the man is coming from. I mean I really understand, in a way I don't usually get fictional characters. So I find it very hard to blame him, even for the obvious screw ups, because in every case, I can't see how he could have done it differently.

Maybe I should go and rewatch John episodes and give him a new chance *laughs*

If you decide to rewatch, do me a favour and try an experiment. Watch the John eps in reverse order: start with The Song Remains the Same and work backwards, bearing in mind that at some point in the first season, he figured it all out. I think you'll find you understand him a lot better.