Effectively, the U.S. Privacy Act does not apply to visitors or aliens, so it would not apply to Canadians. However, with respect to the secure flight program, the Department of Homeland Security has stated that it will mesh together the personal information of foreigners and Americans. This would seem to allow the U.S. Privacy Act to apply to non-Americans.
However, the Department of Homeland Security has also issued a final rule exempting a number of provisions of the Privacy Act in the light of the secure flight program. This rule applies to U.S. citizens as well as to Canadian citizens on an overflight. So the short answer, for all intents and purposes, is that the U.S. Privacy Act would not apply.