Smaller aircraft tend to be less profitable due to several reasons:
1: Higher employee costs: You can't pay your regional airliner crews less even though they make less money than larger aircraft.
2: Blue (connecting) passengers: Unless you are operating a regional airliner between very small airports without a hub, its more profitable to use a 737 or A320 rather than a B1900 or a DHC6 since connecting passengers will fill up the excess seats.
3: Slots: A small aircraft will have to fly the same trip multiple times to carry the same amount of passengers as a larger aircraft which means that you'll use more slots.