Where do you live?
Do you live in New York, Los Angeles, Miami, Atlanta, or close to one of those cities? One of the biggest downsides of being a pilot is having to commute. Do you want your commute to take 30 minutes by car, or 3 hours by airplane?

Both JetBlue and AirTran have lots of aircraft on order, and upgrade times are low. Both look somewhat stable, with neither company really being much better than the other (In my opinion). AirTran pays more, especially now that JetBlue flies the EMB-190. So my primary advice would be to look at domiciles. You can't really go wrong with either of these airlines (Remember AirTran pays more).

Finally, have you considered Continental. I think they are a more stable company (With lots of international flying). They pay much more than AirTran and JetBlue. Upgrade is a little slower, but I would trade some money at the beginning of your career for a lot more at the end! Your free flying benefits are better because Continental flies everywhere. They have U.S. bases in Newark, Cleveland, and Houston. I read they are negotiating for bases in So Cal, the Northeast, and Florida.