It makes sense at one level: frequency

Vacation travelers are flexible and might be happy with one daily option, but the business and premium travelers who are the bread-and-butter of hub-and-spoke will not tolerate a five hour hub sit to make their connection. Airport appreciation is for crews only, not customers.

Even though larger planes are more economical per seat, passengers prefer five or six daily flights rather than one or two. That, combined with lower wages for RJ crews, helps to tip the scales.

Until congestion and/or fuel prices force the airlines to move to fewer, larger airplanes, they will follow market demand. A mainline pilot group which brings RJ's in-house and then charges narrow-body wages to fly them might very well wind up non-competitive.