We flew Air Tran, but we took our son's car seat (he's 39 lbs) so it's a large one. The only thing we had to do was put a tag on it with our name and secure all of the straps, and we checked it with our suitcases.
DH was brilliant and brought a bungee cords with us, so when we got to Orlando, he bungeed all of our luggage together, and bungeeed the car seat to the luggage. Worked great to not have to haul the car seat through an airport, or when we checked our rental car in we did not need help with our luggage.
If in doubt, or you would be worried about your car-seat condition, then call the airline, or put it into like a canvas laundry bag.