Why does the word “Atheist” have such a negative connotation?

Even as an agnostic, watching a video on the American Atheists website that had people saying “I’m and American Atheist” made me cringe and have a prejudice that they’re bad people, but I know they’re not. I either cringed because of the negative connotation or I was shocked at the diversity in Atheism.
http://www.atheists.org/

Topics: religion, atheism, prejudice, connotations, association, implication