We booked a package through AAA through Disney for 2009 and included the air, but then pulled the air out as we found cheaper fliights on our own and could pick our own flights. With air through Disney, they decide when you fly in and out, and it may not be a direct flight. They also charge a lot more (IMO) than what you can get on your own. If you use Disney air and want to make specific requests, that is an additional fee of $50 per person per request.
To me, that is CRAZY! Especially when we booked air on our own for a good rate (about 1/2 of what Disney was charging us) and my TA hadn't gotten my message that we were cancelling Disney air...she also got a message from the airline that we had booked flights AS WELL AS DISNEY in the same names, and which were correct.
SO...Disney was going to charge us $400 per person and what they paid was $220 (which is what we paid).
Long story short...I say book on your own for airfare!!!