Allegiant only flies into the Sanford airport, which is about 40 miles from WDW. AirTran flies into Orlando International (MCO).
If you're planning on renting a car, then it doesn't matter as much which airline/airport you fly into. If you were planning on taking Magical Express, then you will have to fly into MCO, since Magical Express does not go to Sanford. I have flown AirTran numerous times & have had good luck with them. If you can, fly in the morning & if you have to connect in Atlanta, allow at least 1 1/2-2 hours to connect there.