I didn't see the event happen, but here's the gist of a story from the Times about Air Force One (actually, its stand-in) flying very low near Manhattan and Jersey with 2 F-16s following.

This was done as a photo op for a picture of the plane over NYC. A photo op? Of a plane flying low near Manhattan?!? What could they have been thinking?
And, on top of that, they didn't see fit to notify the public about any of this, so people understandably panicked and evacuated buildings (and probably made 8 million cell phone calls). THEY FLEW A 747 AND TWO FIGHTER PLANES LOW OVER MANHATTAN AND DIDN'T TELL PEOPLE. The cops didn't know either.
Bloomberg had a good point: "Why the Defense Department wanted to do a photo-op right around the site of the World Trade Center catastrophe defies imagination. Poor judgment would be a nice way to phrase it."
You can read the Times piece here: http://cityroom.blogs.nytimes.com/2009/04/27/air-force-one-backup-rattles-new-york-nerve/


Salon.com
Comments
By now I was, a) getting pissed, but b) watching her embarrass herself. I said, "It's not paranoia if you lived here when it happened." She was like, "Whatever." And that was her basic argument. Whatever.