Funny, I've always thought that "they hate us for our freedoms" was a joke, and understood as such by everyone.
No. Many do hate Americans for their freedoms.
Many people believe that an individual should not have the freedom to speak out; especially against the government.
Many people think that an individual should not be free to practice whatever religion they want (Islam!).
Many people think that the state is the center of existence, not the individual.
Many people want strong and dominating government that tell people what they should be doing, unlike America where you can do whatever you want, including sitting on your ass doing nothing.