Maybe stats will prove me wrong but from 1996 til 2001 I worked in Toronto (private since 1996) and general aviation was alive as ever. Yes you are right, I am sure that some would not fly if the fees were implemented.
Decision has to be made, do you not privatise to preserve the general aviation? Don't worry about the airlines, they will do just fine since they pass on the cost of the fees to the traveller which intern is only a few dollars per ticket. As for training airline pilots, the US doesn't seem to have a problem in that area. Actually there are too many pilots in the US. Many without work these days that are actually moving to Europe to fly for small regional airlines. So I don't really understand where you have a solid arguement.
1. there is a over abundance of pilots
2. airlines can easily pass the cost of user fees on the the traveller
3. you might lose 10% of your general aviation
You can talk about safety, once again maybe stats will prove me wrong but I believe that Canada has maintained it's best in the world safety record since privatisation in 1996.