Air Force One Fly Over

I am confused about something but first from:

New York Times: White House Apologizes for Air Force Flyover

 Now from Wiki:

Air Force One is the air traffic control call sign of any United States Air Force aircraft carrying the President of the United States.^[1] Since 1990, the presidential fleet has consisted of two specifically configured, highly customized Boeing 747-200B series aircraft – tail codes Special Air Mission (SAM) “28000″ and SAM “29000″ – with Air Force designation “VC-25A“. While these aircraft are referred to as “Air Force One” only while the president is on board, the term is commonly used to describe either of the two aircraft normally used and maintained by the U.S. Air Force solely for the president.

Air Force One is a prominent symbol of the American presidency and its power.^[2] The aircraft are among the most famous and most photographed in the world.^[3]

Now in the eleven years I have been in the military, Air Force One carries the title only when the pres is on board the plane.  So what are they stating?