From the Comments:
Bill Asks: If it was a missile, why cover it up?
US policy at the time was to deny terrorism. The idea being, if everyone thought the plane just fell out of the sky, then no one is scared of angry ragheads shooting at them, and ***POOF*** you've de-nutted the terrorists.
Many think it was this strategery that lead the terrorists to finally attempt something huge like 9/11. They had to commit an act to big to deny.