We've flown them 8 or 9 times with our ASD DS and they have always been great to him. They are one of the low cost airlines but I don't feel they treat passengers any differently that one of the more expensive carriers.
I'm not sure how it would be handled since you are going thru MAW, but they have a business class section & every time we are able to (when there are available seats) we pay $35/seat at the airport at check-in and are put in business class for the extra $$$. Sometimes it is available & sometimes it isn't. Just makes for a little more relaxtion on our trip to WDW or back.
One thing that has happened alot with Airtran lately is their flight schedules have been changing. They've recently added new cities and that shook things up a bit. People on the Transportation Board here have a lot to say about that and I just wanted to mention it in case you venture over there. Mostly it is cancelling a flight and re-scheduling it for a different time that day or changing flight times. They will notify you if you flight time changes but it appears that their schedules are pretty well set.
A mom in our support group with a severly autistic son said they have a special assistance coordinator who will help to make sure you have help (if needed) when boarding, inbetween gates, etc... I had not heard of it before but perhaps that would be a good resource if you need it.