I think especially the routes where you have many connecting traffic from long-hauls don't make a lot of money because the sectorwise revenue is very small if you compare it with the normal price including intl. sectors. Lets say LHR-KUL-PEN vv. for 1000USD gives 460USD for LHR-KUL, 20 USD for KUL-PEN and 20 again for PEN-KUL and 460USD for KUL-LHR. (figures just as example) and as you see the USD 20 would be much lower than the normal fares.
The routes where they could do money is on the once where they have a lot of point to point traffic because they mostly have to pay fullfare but this might change with the AirAsia low fares.
With the rural air services I full agree, especially when I consider that I flew alone in a Twin Otter from KUD to BKI!
Unfortunately you only see them during Hadj season and they are only leases, same goes for the MD 11 they had for Hadj flights. Would love to see them with some long-hauls but lets dream