Passing thru,
The key phrase is "per seat mile". I don't know what actual costs are; I was just guesstimating. But it's a fact that RJ unit costs are higher than mainline equipment. Why? Fewer seats to spread costs across. Sure the aircraft are smaller, don't burn as much fuel, and the crew is paid less, but they also have one third the number of seats as, say, a shuttle configured A-320. So the A320 could cost twice as much to operate, but since it carries three times the number of seats, unit costs will still be a third lower than those of the RJ. That means that either load factor doesn't need to be as high, or fares don't need to be as high to break even as opposed to doing the same flight on the RJ.
Here's an example, for a fictional 200 mi flight flight:
ERJ-145: $1500 total cost / 50 seats = ($30/seat) / 200 mi = 0.15 per seat mile (CASM)
A-320: $3000 total cost / 150 seats = ($20/seat) / 200 mi = 0.10 CASM
So you can actually spend less money to operate a flight on an RJ, but still make less money than if you use a larger airplane, all because the unit costs are higher.
In a market like the shuttle, maybe it makes sense to use a smaller airplane, since the loads are pretty pathetic. But it would make even more sense to use the airplanes where there is actually a demand for the product. There is no demand for more seats on the shuttle routes, so if you are ever much less than about 90% full, you're losing money. The other guy at the same time can be 60% full and making money. They have more seats to spread costs across. Do you see?
I can understand your confusion, since the conventional wisdom is that the RJ is the end-all, be-all perfect cheap jet that lays waste to all competitors. It is an important part of a full-service airline's fleet, but only within its own niche. It is not cheaper in all things, or in all situations, otherwise you'd just replace mainline aircraft with the equivalent number of seats worth of RJ's. That's not happening, and never will.