Looks to be fixed this morning.

Yesterday when I was booking a trip (not an AirTran market) at work, the online booking tool had a splash screen message that AirTran flights would not be available from (if I recall correctly) 9:00am to 12:00pm CDT, and this was at about 2:00pm CDT.

That suggests there was some upgrade or other planned outage, although probably an emergency one for them to do it during the day on a weekday. Perhaps that's tied in to the website issue?