People often mistake their shyness as arrogance. People have a tendency to assume the worse. Being shy and being arrogant has it's commonality that they don't talk to many people. For shy people, it's obvious why they don't do that. For arrogant people, they don't want to talk to just anybody because they feel that they are too good to talk to certain people. That's one common reason why shy people get so much hate.
Another could also be because that shy people are so socially awkward. Certain people like to pick on those who are awkward like that because they think it's funny.