'Why are atheists thought ill of?'
Vocal atheists are thought ill of because they are as annoying as their theist counterparts. Often times, they have so much invested in making people "see the truth" that they overlook the significance of belief to the believer. As someone standing outside the debate (as Costrin so astutely pointed out I'm an agnostic apatheist...or maybe it's an apatheistic agnostic...needless to say I couldn't give two shits less about the existence/non-existence of a god/goddess/gods) atheists look as obnoxious to me as any other proselytizer. Why the atheist feels the need to shove his/her truth down the throat of the theist is completely beyond me. Can't they just be happy knowing they have "the truth" (whatever the hell that is)?