First soccer game I got into was FIFA 2002. My buddies (playing with Madrid and Arsenal) would wipe the floor with me, until I started picking Bayern. My ethnic heritage is primarily German, and I can trace my ancestry back to Catholic Bavarians. Of the places I've visited in Europe, that region is among my favorites.
So that's why I root for Bayern. I totally get the hate; they're basically the Yankees of Germany. But I don't live there, and it's difficult to follow the Bundesliga as a whole, so that hate doesn't have much purchase on me.
It's interesting that "capitalist" America produced the NFL, with salary caps and draft rules that make it remarkably difficult for one team to stay on top for long, while "socialist" Europe's transfer market is ruthlessly free enterprise.