Actually, all other costs being equal, average CASM is driven down the greater the average distance the aircraft flies. CASM = total costs/available seat-miles. If you put more seat-miles in the denominator, costs being equal, average CASM gets driven down.
What probably happened is one of a few things, and I suspect it had NOTHING to do with fuel costs as, on average, you're paying high average fuel costs no matter where you go. Further average fuel costs per ASM go down the longer that you fly. That fuel cost thing was just a lame "sound bite" for the media to explain away a failure of the airline to make money (or enough money) on those routes.
One of probably a couple or few things happened. One, demand on those markets was just plain low and it was unprofitable. Two, demand was high, but they weren't netting much money, per passenger, for that long distance flight make sense.
For example, let's say Skybus managment figures out that flying CMH-BUR that they can make $10 net, per passenger flying that route. They also figure out that they can make $10 net, per passenger, flying CMH-NH (wherever they fly in New Hampshire, I forget.) Well, if you're going to make $10 bucks per passenger on a flight, you're much better off flying that aircraft a shorter distance and doing that flight several times per day than you are doing that longer flight once a day to make the same money per passenger. In other words, if you're going to make the same total profit flying a plane a shorter distance as you do a longer distance, you're better off flying multiple shorter legs than fewer longer legs per day.
That's why I suspect they dropped those long distance flights.
You explained it much clearer than UAL. You are right when you say that, all costs equal, more seats drives down CASM. I was referring to the fuel now versus the fuel back in the Indy days and how those prices affect the optimum range of the aircraft based on CASM and RASM (which I forgot to throw into the equation there). You are also right on when you alluded to say that if Skybus is receiving a lower RASM than another carrier on the same coast-coast route, it would need to better match that RASM to the distance (ie, shorter segment w/ higher frequency). In Skybus' coast-coast case (and I presume Indy's as well), they were operating below the optimum RASM for that segment and could not make up for it in frequency. Good insights.