Right now I'd say the 49ners are most hated mainly because of their fanbase and their coach. I can respect an opposing team, even a division rival, when they are good and back it up, but what the niners have done has IMO crossed the line into douchery. That and I get sick and tired of hearing how much better a team is supposed to be now from games that were played 20-30 years ago.
Starting this season, I have also grown to really despise the Colts. Mind you, I respect the Colts as a good team, but some of the sheer ignorance, media fawning, and highly selective (and wrong) memories has really set me off. I would like nothing more than to see the Colts crash and burn.
I used to dislike the Cowboys and Steelers, but honestly, I don't think either is worth the energy any more. The same applies if not more so with Washington. I haven't forgotten last year's douchery during the playoffs by some elements of the Redskins fan base.
Another team I am starting to dislike are the KC Chiefs. Mainly because seem to have "short man syndrome" and want everyone to think they are better than they really are. We'll see how that goes (I expect the Chiefs to finish 11-5 and lose their first playoff game).
Anyway, just my take.