I don't think flying through Canada is such a crazy idea. Statistically, I'm sure you could make the case that there have been fewer terrorist attacks both on Canadian carriers and on international carriers traveling through Canada.
I don't know if Canadian security is any better than the U.S., nor do I doubt that Canadians are equally as horrified of Tuesday's events. The point is that the U.S. and all it's assets are and will probably continue to be the prime target for terrorism simply because of what we represent (capitalism, oppression, hegemony -- however the terrorists choose to label us).
That said, I will not be going out of my way to travel through Canada simply because I still think flying in the U.S. is incredibly safe, and will become even safer in the weeks and months ahead.