I grew up hating a lot of teams.
It was never the 49ers. They were in a different conference, and since they were the "good" guys in the good vs evil thing with the Cowboys being the "bad" guys - it was easier to root for them.
Of course, when we became rivals it was on. But we were both teams that played physical tough football in a league that was moving away from that. I had a lot of respect for what Harbaugh did at Stanford, and his stop before that. And it was a hell of an accomplishment to beat those guys - because they were beating up other people.
It was the two titans of the NFL for a while, but then the rivalry got crazy and people started taking it personally. When they slipped I admit I was pleased because they were a big roadblock to continued success. I didn't expect we would slip like that a year later.
But once they fell out of contention, the worry over them was over. Then it just got weird. We had a lot of our fans almost dancing on their graves. I can see Seahawk fans hating Denver, they repeatedly screwed us. Or even the Raiders, but where was there enough background to hate the 49ers this much when they were really only a rival for a 2-3 years max?
The weird part is that all the dancing on grave almost karmically screwed us, because people were literally filled with glee about all the things destroying Kap - and almost oblivious to the problems we were having/going to have.
I think we are a better team but after all those years of crappy owners by Seahawk, Mariner and even Sonic teams (the Sonics not as bad until they started drafting teams of all centers to destroy the fanbase enough to move them), you would think this region if any would at least feel for the 49er fans that are getting shelled by crappy ownership decisions.
I don't even think the 49er fans that everyone hates are actual 49er fans, just rudderless 49er/Raiderfans that travel in packs toward whatever team is doing better.