Because they supply feed to the hub. Lose money on the feed, make money on the connection. The original concept of the RJ was to connect smaller cities to the hub which previously had been flown by turbo props.
Continental has reduced it's total 50 seat fleet and will continue to do so in the future. The 50 seat jet was a product of $28 a barrel oil in the early ninties. Continental ordered 275 (with 100 options, that they have not exercised) of the EMBRAER flavour in the guise of Continental Express. They now operate 239 between XJT and CHQ, that would be a fleet reduction.
Delta needed to replace 10 aircraft operating out of LAX, no net gain.
Midwest, who knows, maybe they cannot afford new mainline aircraft.
Compare the CASM of a 50 seat RJ to a 137 seat 737 over a stage length of 300 miles, you will see that the 737 wins by a large margin. The longer the stage lenth the better the CASM number for the 737. As long as the Majors continue to utilize the hub and spoke system they will need feed. However, on shorter stage lengths the turbo prop will make a comeback now that "The all jet fleet" mantra has worn thin. I see Continental will operate Dash 8 aircraft in CLE, makes sense, cheaper, you see. There is is also a scope issue at Continental that prevents it's feeders from operating larger aircraft and right now there is a wait time for 70-100 seat EMBRAER/Bombardier fleet types. XJT's CPA with CAL guaranteed a profit and included fuel. Horizon operates Q400's on the west coast and Frontier will soon operate a few out of DEN. See a trend here?
As the cost of operating a 50 seat RJ's continues to esculate so will they be parked as contracts come to an end. The turbo prop is poised to make a triumphunt return.