I've never understood the hatred directed at Shinji Ikari; he may not be the archetypical hero, but he is nevertheless an amazing protagonist, if one factors in the vintage of NGE. Instead of an up-beat brat who can't wait to lay waste to the enemy or an angst-ridden teen who can't get over this one traumatic experience in his past (murdered parents, witnessing a brutal homicide, losing at scrabbles etc), we have a protagonist who actually seems real, for all his apathetic depression. I'd put him ahead of -any- protagonist influenced by the above (partially or not), and that includes pretty much anyone from a shounen show.
Having said that, the purpose of this thread was to name your most hated character. This is problematic, since I tend to drop series where I simply can't stand a given character (if this happens to be the protagonist, it's a given). I'd probably go for Light of Death Note fame, since the megalomaniac narcissist made me drop the show; a pity, since the concept was great, but five episodes of monologues from God's gift to man and an exposition hell that makes Goodkind seem sane was simply too much to bear.