That is a GREAT question. At this point, the only evidence we have is photographic evidence. What it comes down to, then, is our interpretation of the photographic evidence. And I've posted a half dozen pictures on which no one has commented.
But this lack of evidence in itself raises a set of disturbing questions. Why wasn't the WTC site treated as a crime scene? As far as I can tell, folks went in, sealed things off, and starting shipping out debris to China and Staten Island almost immediately. Why did federal agents immediately confiscate all the security videos at Boston Logan and the Pentagon? Surely it would have been nice to see videos of the alleged hijackers getting on the planes. And why was information from the black boxes on the planes never released? Why all this secrecy, if there's nothing to hide?
To the gentleman who was an eyewitness to the Pentagon attack: I believe you. But I think a perfectly reasonable explanation is a combination of a real plane (for distraction and plausibility) and a missile. There was no plane crash in DC.
By the way, while you were there, did you happen to see the E-4B flying overhead? That, too, was observed by hundreds.