That is fairly typical. They are not the busiest of flights outside of the peak summer/Christmas seasons and unless there is a major event happening on the mainland or the Islands. The flight costs are comparable to driving or getting the train to Wick/Aberdeen/Ullapool to catch the ferry and obviously have far more convenience, and that's just the EDI routes.
I think local residents still get a certain discount on flights to mainland Scotland and I believe children get x number of flights or ferry crossings for free per year, to help with the high cost of running them.
The air discount scheme operates for residents of the islands to subsidise the cost of getting to the mainland and has been approved until 2015 by the EU.
It offers 40% discount on core fares (excluding PSO routes which are subsidised anyway)
Apparently it is cheaper to book BA even when using Loganair (at least it used to be anyway).
Ex