What bugs me the most is that I can't really tell why I dislike him. I suppose what Sam accused him of in the second season's premiere, that he puts the hunt and his need for revenge above everything else, hits too close to home for me. Of course it always has something to do with preparing his boys and protecting them like that and yeah, it's a big part of what defines Sam and Dean especially. I didn't get why he left them on their own in the first season and I still think, even though it's heartbreaking and all, he is a bit of a dick to burden Dean with the whole burning in hell for him thing and the 'Hey, kill your brother, will you' thing. (I know I'm being a little unfair here, sorry...) So, Evil!Dean's accusations in "Dream a little dream of me" again didn't feel like an assasination of the character at all to me but again, too close to home. Frankly? I dunno :( I want to like him, or at least to understand him and try to read epiphany-provoking fic with him, but so far, no luck...

Sorry, for editing but I re-read your comment and this And Dean & Sam clearly are lost without him, which speaks volumes about the positive impact he had on raising them actually is my big problem with him and there I'd contradict you: As a father I think he should've prepared them to get by on their own, to help them grow up and be strong and make their own decisions. The fact that they (esp. Dean) are lost without him, or at least at first, speaks volumes to me that he didn't do his job well.