RJ's are profitable if they are properly utilized. We see what happens when airlines use them to compete in low yield markets (Indy Air), but most customers flying an RJ pay massive premiums to travel to small market airports. MLB, AEX, AGS, ILM, etc are a few examples of typically very high yield markets that RJ's serve well. Hundreds of other markets are out there that RJ's are profitable on.
At this point, there are far too many RJ's for them to all be profitable. Thus the move to reduce RJ flying. RJ's of all sizes are here to stay though. 50 through 90 seat RJ's all serve niche markets and will make money once the parent companies figure out how to use them all to their designed potential.