There are legitimate questions about the events of 9/11. I recommend a visit to this site:
http://911review.org/ScholarsforTruthabout911/
It is unclear what struck the Pentagon but it was not a commercial aircraft based on the evidence. One photo shows a part from a JT8D turbojet engine, consistent with an aircraft unlike the one that was claimed.
The Editor In Chief of the 125 year old monthly magazine, Fire Engineering, called the investigation into the Twin Towers collapse a farce. ($elling Out the Investigation, January 2002)
Ed