There's also a question of frequency, as some airlines have sparse schedules of non-stops but supplement those with one-stops (e.g. EWR-MCI on CO vs. EWR-CLE-MCI). And what about mixes with other partners (e.g. EWR-DTW-MCI on CO/NW)? Being able to offer a lot of different times is important for attracting business travel.

There's also a real competitiveness issue, as many of the larger cities, like ATL, are hubs. DL and FL fly a lot of non-stops, so if you're a non-hub carrier competing with them you have to offer connecting flights to most of the same destinations (except your own hubs). You've already got a disadvantage because the taxes on yours will be higher and it'll be more inconvenient, so it seems the FF miles are useful competitively to compensate.

The flip side of what you're saying would seem to be NW and its one-stops, such as ATL-MSP-Fargo, where the "1 stop" in MSP involves a change of aircraft and the same inconvenience level as a connection, but you get credited only as if it were a non-stop.