In short, it's because of complaints about noise. From the Canada Gazette, Vol. 132, No. 2, pp.98-103:
The regulation reflects the Minister’s desire to have increased
oversight of sightseeing flights within the Québec/Jean-Lesage
International Airport control zone.
The regulations are
intended to prevent frequent low level flights for aerial sightseeing
purposes over the built-up area within the Québec/Jean-Lesage
International Airport control zone and to stop commercial
passenger-carrying aerial sightseeing flights from using the Lac
St-Augustin, Quebec aerodrome for either take-offs or landings. The
prohibition of low level commercial aerial sightseeing flights within
the entire Québec/JeanLesage International Airport control zone is
intended to ensure that such operations do not relocate to another
nearby lake and recommence sightseeing operations from that location.
Since the late sixties and, increasingly, in recent years,
Transport Canada has received numerous complaints from citizens about
the noise of floatplanes flying over several towns and cities in the
Quebec City area.
The Gazette goes into a lot more detail about the background, impact, consultation process etc. 25 local mayors signed a letter to Transport Canada asking for action, so I guess it came down to political pressure in the end.