ATA for many years earned their keep as a charter carrier. Flying military charters as well as for major travel agencies (Pleasant Hawaiian Holidays). A few years ago they decided to make a go at operating scheduled passenger service with their fleet of 727's/757's/L1011's.
IND and MDW were primary bases with flights to Florida and the west coast. There was really no hub and spoke type operation to their network.
Chicago Express has operated as their commuter operation for some time.
As far as a mileage program, I think they have a program, or at least I read about a segment based reward program for frequent flyers that they were trying to implement.
Currently ATA flies into LGA, BOS, LAX, DFW, MDW, IND, MCO, I think RSW with scheduled service. I'm sure I'm leaving out a few cities, including some Mexican and Carribean destinations.