In my opinion, Hollywood would have rewarded it with a nomination for best picture, and probbly the Oscar as well, if Kerry had won. Unfortunately for Michael Moore and the America-haters in Hollywood (and fortunately for the rest of us) Kerry lost, and F 9/11 is credited for helping Bush as much or even more than hurting him, ergo, Hollywood would just as soon forget the whole matter.
I don't think it's that complicated. F911 wasn't nominated for Best Picture for the same reason a Best Animated Feature category was developed: people in the film community didn't like losing one Best Pic spot to "outsiders" like animators, when they could use that spot to nominate and award potential or past employers. Also, the feeling I get out there is that people think F911 is yesterday's news and has gotten plenty of awards and notice.