I am flying AirTran, too, and just checked their policies yesterday on this:
Directly from their website...
"You may bring a stroller to the gate for ease of travel through the airport. The stroller may be gate checked just before boarding the plane and will be returned to the aircraft jet way upon arrival at your destination. Car seats and strollers may be checked free of charge; any other items are subject to standard baggage fees (i.e., portable crib, high chair, etc.)."
...I'm a little apprehensive to check his car seat, but I might ask if I can take it to be gate checked with me as I believe at 5 months he will still be in his carseat on his stroller.
Anyone checked a car seat before? I worry about it getting broken from mishandling.