I wasn’t meaning that RJ’s should pay more than mainline, they just should pay more per seat than a mainline. I generally don’t have a problem with RJ’s, but in this instance they are an inefficient use of a scarce resource (landing slots).
Also, using RJ’s for point to point flights is rarely profitable. Majors just often use them that way as a way to compete against an LCC entrant. Their profitable use is to increase the catchment area of hubs, allowing flights that weren’t available with props but didn’t have the traffic for a mainline (such as IAH-GRR or ITH-ORD). This increases the effectiveness of the hubs and allows airlines to eliminate secondary hubs that primarily served props. However, JFK shouldn’t be acting as a hub. It’s an international gateway and they should really just be running RJ’s to feed into and out of those international flights.