I was in North America on September 11th 2001. I clearly remember that it was initially reported that an airliner had been shot down, however, the story was quickly changed to the official version of events i.e. the passengers over-powered the hijackers and the plane went out of control and crashed.
I think both things happened, suppose that the passengers had regained control of the aircraft, how would the military have known this? Even assuming one of the passengers could fly the aircraft and operate the radio would the military really believe that this was the case? remember, at the time, no one could afford to take any chances, the Pentagon and WTC had already been hit.
It is unlikely that the US government are going to admit that they shot down an airliner for obvious reasons.