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.