I really dont think the CFL has a flagship franchise. There are teams that can make a good case, but then the Toronto media says the Argos are the flaghship franchise, and lets face it, if there were no team in Toronto, the CFL would get far less national exposure if a team did not exist there.
In terms of success on and off the field, you could make a case for the Edmonton Eskimos. They have won numerous Grey Cups and are a first rate and classy organization, top to bottom.
In terms of rabid fan support you could make a case for the Saskatchewan. They draw fairly well in opposing stadiums. A friend of mine from here went to Commonwealth to the store there, and the clerk told him that Rider gear outsells Eskimo gear. A lot of Rider Priders are spread throughout the country, so they tend to go to the games when the Riders are in their adopted city.
Those are only 3 examples , but if you took the time you could make a case for every team. Really all the teams could be considered equal, they all contributing to the new success the league is experiencing, so for any team or the media in that city to make that claim is just arrogance on their part.