I think it's perfectly legitimate to like a team other than the home team so long as it's not for the reasons espoused by Justin.
For example, here in Montreal there are a lot, and I mean a lot of Boston Bruins fans (as well as other teams). The reasons for this are largely due to familial allegiances, i.e. father grew up watching the Bruins and the son(or daughter) is carrying the torch so to speak. Or, I knew someone a long time ago that was a huge Red Wings fan because he idolized Steve Yzerman.
This is ok in my book, but to say that the 49ers and Raiders are garbage and therefore not worthy of your loyalty is complete B.S.
Justin, in case you didn't know, the fortunes of sports teams are cyclical. When the 49ers were in the middle of their dynasty the Cowboys were experiencing some very challenging years. In 1988 and 1989, while the 49ers were winning Super Bowls, Dallas went 3-13 and 1-15, respectively. So, using your logic who was garbage then, and who would you be supporting? The Cowboys are good now but they inevitably will experience a downturn sometime in the future and at that point what then? Will you continue to support them despite being garbage or will you switch allegiances.
I have been a longtime 49ers fan, for almost 20 years, and I have continued to support them through thick and thin. This, in my opinion, is the essence of being a fan—going through the bleakness of the lean years to eventually experience the euphoria of the good years.