It's strange they don't comment about their own products like single malts or Harris Tweed clothing, all of which seem substantially highly priced.
The various carriers serving the islands over time seem to have made minimal margins, and really not much of a return on capital. Aircraft mostly have to be secondhand. I doubt that ATR or Bombardier, as current main manufacturers of local service propeller airliners, spend much time with Loganair.
These sort of stories often tend to emerge in August, during the brief tourist season. Look at the loads they get up there in February, along with all the costs of weather diversions and cancellations, which get them not a penny of extra revenue.
Anyway, there's a long tradition of whinging up there about transport links (and probably everything else). I recall back in the 1970s there was a magazine which always contained pages of whining about Caledonian MacBrayne, the substantially state-subsidised shipping operator there. There was also, after a private enterprise company built the first bridge across to Skye, a vitriolic campaign against their levying tolls (the same as the replaced and unreliable adjacent car ferry), to the extent that one of the companies involved, who I was involved with, had to mount substantial security precautions around their premises.