It was changed to AF1 a while back. I can't remember why.
The President didn't want to be known as Steak sauce...
keep in mind that there that AF1 is different from AF1. (confused you already, eh? read on).
Don't get confused between the ICAO code for Air Force One (AF1) and the IATA code for Air France 1 (AF1). A controller's strip will (should?) never have AF1 listed for Air France 1. That should always go in as AFR1, as AFR is the ICAO code for Air France. As the common passenger will generally only see the IATA code, AF1 will always be Air France 1, whereas the strip will be AFR1.
That is one of the reasons the strip for Air Force One is AF1. Also, the POTUS doesn't want to be known for Steak Sauce. Free advertising, you know.
PS. Also, to my knowledge, there has only been one time in modern history when Executive One has ever been used, and that was on a DC10 flight after some major incident, IIRC. May have been from the aftermath of AAL191..?