Why do you say that? Airtran, Frontier, Southwest and Spirit were around in the 90's when the legacies were steamrolling, so they are making money again, thats great!
With the exception of Southwest, the other airlines that you mention were not around very long. If you look at the mid-90's, each of those airlines were very young and each was flying a fleet of older airplanes. AirTran and Spirit were flying older DC-9's, and Frontier had several 737-200's. Those fleets had to be updated, and that meant taking on a lot of debt to be able to do that.
The LCC's of the nineties operated smaller, older fleets over a much smaller route network. Fast-forward 10 years, and these same companies have a lot of debt because of expansion and employees remaining longer. Because of employee longevity they are demanding more pay and benefits. The fleets are more fuel efficient, but the capital required to acquire those fleets comes borrowing a lot of money.