Also, all things equal, there is an optimum range for each aircraft, and frankly, coast to coast in an A319 might push the optimum range (as far as CASM is concerned) down when fuel prices are high. When Indy ended their coast-coast service, fuel costs were much lower (especially if they hedged), so there was more than meets the eye in that situation.
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.