I believe it was shot down AND that the story of the passengers is probably mostly true -- I don't think the two stories are mutually exclusive at all. However the passengers were unfortunately not successful in overtaking the hijackers before it went down. This site hasn't been updated in a while, but check it out:
http://www.flight93crash.com/
Like some of the previous posters, I don't think we'll ever find out the truth for sure, if we havent already. It's not like it's something the government would ever admit.