I haven't seen it pointed out yet on any of these AF1 threads that all active AF pilots fly x-amount of hours a month to keep their proficiency up and that includes the Air Force 1 pilots. The money for this flight was already in the defense budget so there was no extra expenses involved.
The problem is a political one. Obama's shortsightedness to see that a low flying 747 with trailing F-16s over NYC would invoke memories and terrorist concerns.
Agreed that there was probably no extra expense for the planned flights. The extra expense on the ground in NYC and nearby NJ was substantial, however — lots of extra police time, lots of ambulance runs and hospital personnel to treat people injured, feeling faint, having chest pains, having PTSD flashbacks, etc. And the New York Mercantile Exchange was evacuated during trading hours, at an impossible to calculate cost.
Spoken like a true government worker!
The problem is a stupidity one -- how many people were involved in setting this up, and it didn't occur to any of them to make sure it was announced in advance?