I left corporate aviation to come here. I like it fine. The corporate flying is more fun, but the ability to bid a schedule, swap/drop and be able to "leave all your troubles in the bag room" when you go home are hard to beat.
At Airtran, you can live where you want, and since the average corporate job lasts 3 years, you generally need to be willing to pack it up and move if you want to keep moving up, unless you grew up in TEB (shudder).
If you want to go with the corporate job, make sure to learn:
1) How many pilots per airplane. Anything less than 2.5 and you can't be covered for hard days off, training, vacation, etc. Accept no less!
2) How much severance would you get if they close the flight department tomorrow? I would be looking for 3-6 months guaranteed. If they say, "We'll never close- we're too valuable to the company" then they really don't have a clue.
3) How much flying is for the company, and how much is weekends and holidays flying the families around? Herein lies your misery ratio, if you have a family of your own. If they want you to fly them places on the holidays, would they be willig to airline your sorry @ss home to be with your family? It's usually cheaper than a hotel . . . and if they aren't willing to do that, you probably don't want to work for them anyway.
My personal guess is that versus a Fortune 500 company, it's a no-brainer. Go with AirTran. You'll have more time off, great training, plenty of fun, and never have to answer your phone on your days off. You can always leave for another airline or corporate if the right one comes along, and you don't like it, but I haven't seen any former corporate guys leave here to go back, that's for sure.
Now, if it is a Fortune 100 company, in a town you want to live in, and they staff appropriately, don't skimp on the training, and offer bennies comparable to what the execs are getting, well, then, you do have a dilemna, don't you?
Good luck.