Don't forget that most passengers only take a commuter aircraft to get to a major airport where they get on a larger and more efficient aircraft that takes them to their real destination. So even if the mainline carrier loses some money on the short commuter flight, they make up that money in the more expensive tickets on the larger aircraft those commuter passengers go onto after. Instead of looking at the efficiency of the commuter aircraft, look at the efficiency of the total trip each passenger books.

Those 135s are already paid for/being paid for, so if there is enough demand you are better off putting those aircraft to work to feed larger international flights even if you are losing some money on the first leg.

Also, some markets are so competitive that carriers are willing to lose money on flights just to deter competing carriers from entering a particular market.