Connecting flights often cost less than a non-stop because most people prefer non-stops.
I can think of three reasons airlines allow unnecessary connections:
1) Tickets can still be sold if the non-stop sells out without having to update the routing rules.
2) If frequency is low, and someone prefers a certain time of day even if it means connecting, that's another ticket that can be sold.
3) There just aren't that many people who "abuse" the connections.

FT has a lot of followers, but there are still far more non-FT airlines passengers.
AA seems to have more strict routings than other airlines for domestic flights.