Airtran does have e-tickets if you book your flight directly through them. If you arrange your airfare through Disney you get paper tickets still. We have flew with them last year through Disney and received paper tickets. This year we originally booked them again through Disney and received paper tickets.
We actually ended up having to send the paper tickets back to Disney because we canceled our air reservation with AirTran through Disney. AirTran has a bad habit of over scheduling flights and then canceling them in bulk as your travel date gets closer. Last year they rescheduled our flights 8 times over the course of the summer.
Fortunately all the re-scheduled flights worked out in our favor time wise. This year, they re-scheduled us all on connecting flights through Atlanta. It makes for an 8 hour flight from Philly. Heck, with waiting in line at the airports etc. for a few hours extra I could drive.
So we called Disney and because the airline canceled our original flight, and we were not getting what we paid for any longer, we were able to cancel our non-refundable tickets. We just had to send the paper tickets back to Disney.
Disney said that AirTran is the only airline that does not issue them e-tickets for a package inclusive with airfare. Who knows why as waiting in that long line to check in is such a waste of time.