Actually the USAF was in full effect, if you lived in NY. There were F16s flying overhead all day, and I can assure you, they leave an impression in terms of sound decibels.
They were about 5 minutes out of catching the 2nd plane, they knew there were terrorists aboard but they had quite a catchup journey from the airforce base (I believe located in Rhode Island). No one really wants to know what their orders were, if indeed they had caught the plane before they were over civilian territory. Some questions are sensibly avoided in times of a national tragedy.
The still running conspiracy theory is that they actually shot down the plane that crashed in the boonies that was headed for washington.