The only "excess" government fees and taxes specifically imposed for travelling transborder come from the US government, not ours. There are no additional Canadian government charges imposed on transborder or international trips than are charged to domestic ones, albeit the security inspection fee on the return segment is actually much less than the $12 imposed on the outgoing segment. So in this particular case, blame Washington, not Ottawa, FlyerAl!
Another benefit YHM has over most other airports in Canada or the US is its current lack of a facility fee tacked onto the cost of the ticket. But since the YVR folks are running the place, it can only be a matter of time: Hmmm $10x5million...