It may raise some questions, but it doesn't really make me think that there's a government cover up. To believe this conspiracy, you have to believe that the CIA, FBI, DC police, Department of Defense, American Airlines, FAA and countless witnesses are in cahoots to cover this up. You also have to discount all the frantic cell phone calls from passengers.
And above all else - my question is, what would be the point of covering up the fact that it was a missile or small plane instead of a 757?