This is not true for all flights to/from Canada, of course, but it does add complexity, expense, and often travel time for people who want to deal with Canada while avoiding US authority.
Overflight of US airspace doesn't give the US authority over the people inside the airplane. And flights to Canada from Europe or Asia don't overfly the US, except perhaps Alaska, but that's of zero consequence.
You're right that many direct flights between Canada and Europe or Asia don't overfly the US. Many of the affordable options are via US connections, however, and travelers from the rest of the world to Canada frequently overfly the US.
As for Alaska, it's very much a part of the US, to the level that everything I said above is true for flights which only overfly Alaska and none of the rest of the US.