This is actually a question that I feel has been around a lot. Being a northerner myself, residing in Norman Wells, I know the exact same feeling. I can't speak for any other airline, but one thing I notice is that flights into the north are typically less frequent and have either a combination of cargo and passengers or just have, I believe, not as many seats. Flights from Ottawa to Winnipeg are maybe more frequent, and there are more seats on the plane.
We constantly get asked, “Why are your prices the way that they are, when we can go to Europe for three times less the price?” Really, I believe it all comes down to the number of seats that are on that plane and how frequently that plane is flying.
Also, up in the north, companies really have to look out for these surprise costs that come out of nowhere. I think it was in Kuujjuaq where they had the same situation that we had last November, and are in right now, of having a surprise fuel shortage: There's no fuel available. When you're going those long distances, I can only imagine—although I can't speak for them—that this has a lot to do with it, and to go those long distances I think would drive the costs up.