Maybe the passengers took it down. Maybe they didn't. But if a hijacked plane is not communicating and responding, especially in the midst of all of the #$%* that happened that day, then it needs to be taken down. It is horrible that those people had to die, but in doing so they saved the lives of countless others. If I was on that plane (or a loved one), and I couldn't do something about the situation myself, I would rather be in a smoking hole in a field than a smoking hole in D.C.
If the US Government shot that plane down, it wasn't for the fun of it. They did it because they had to. And if they covered it up by saying the passengers took it down, then that's even better. In doing so they gave a little honor to those poor people who died so that others may live. What story would you rather remember?
There is crap that goes down everyday that the government doesn't tell me about. I'm glad. I don't want to know where our troops are going to invade tomorrow. Or how we just missed nuclear war by 2 seconds. There is some #$%* that we just don't need to know.