Interesting 911 article citing columns by William Safire and Robert Novak right after the attacks.

William Safire:

The most worrisome aspect of these revelations has to do with the credibility of the "Air Force One is next" message. It is described clearly as a threat, not a friendly warning—but if so, why would the terrorists send the message? More to the point, how did they get the code-word information and transponder know-how that established their mala fides?

That knowledge of code words, presidential whereabouts and possession of secret procedures indicates that the terrorists may have a mole in the White House—that, or informants in the Secret Service, F.B.I., F.A.A. or C.I.A. If so, the first thing our war on terror needs is an Angleton-type counterspy.

Robert Novak:

“Security experts and airline officials agree privately that the simultaneous hijacking of four airliners was an ‘inside job,’ probably indicating complicity beyond malfeasance.”

This site however shows that the use of the code name "Angel" for Air Force One was not exactly a secret.