Racism, jealousy, fear, those are probably the main reasons why people hate Jews. The jealousy arises from the fact that many Jews are very successful, and Jewish parents tend to heavily stress education so Jews are often intelligent and educated (which probably helps with the success too). For the yarmulka-wearing and orthodox Jews, the clothing makes them different, and people tend to fear what's different from themselves. The racism, well, that comes about just because some folks are racist assholes.

Honestly, I've never really understood the persecution of Jews myself. Yeah, they have some different customs or whatever, but so what, I don't see why that's a big deal to others. It's not like Jews are out there trying to force their customs on anyone else, or convert people to Judaism.