Your right, it doesnt explain it. The only thing I can think of is that they view these routes as feeding a more profitable route or they figure they will take a loss on the route to ensure that they have enough frequencies to satisfy business customers / contracts. They constantly tout the network as their value to customers and one key reasons for the merger, so this could be part of it.
RJ economics aren't comparable on a seat-mile to seat-mile basis. RJ's are one area where there is great sensitivity to comparing the stage length with comparable mainline flights. A 200 miler vs 1,000 miler, with taxi time on both sides, a climbout on both sides, landing fees, etc. will look a lot different.