Well, the "ditch dweller" argument has some appeal, and you can certainly see evidence of it by looking at most of these companies. I would say that CO has some advantages, mostly due to good managment:
1) Labour relations: Most of the so-called ditch dwellers have a serious problem in that they are forced by their unions to pay Big 3-type wages, but without Big 3-type profitability. The specialists (Southwest, jetBlue) are profitable in part because they effectively manage their labour forces through profit sharing and other incentives for performance which are alien to the big players. CO, despite being in the ditch, has very positive labour relations much more in line with those of the specialists.
2) Yield management - CO is the master. Maybe it's because the rest of the top 6 have less streamlined fleets or networks, but CO manages yield like nobody's business - and it shows in the fact that none of the rest of the top 6 are profitable right now.
3) EWR hub - This near-NYC hub is a huge asset, and they capitalize on that asset through aggressively dealing with the many corporations in the region to guarantee a large share of their air travel. Now that strategy is not foolproof, as we've seen with some recent rebellion against CO's strong-arm tactics with corporate partners. But still, they are the dominant carrier in the biggest market, and that is worth a lot.
Will these and other assets keep CO profitable over the long run? I don't know. As the Big 3 get bigger, it will be easier to put the squeeze on CO, and there are already hints that labour may be getting tougher. They're not in an easy position, but they are the best managed major (possibly after Southwest) in the sky.