Catholic and Protestant school boards were created for Ontario in the BNA act. At the time Catholics were a persecuted minority in Ontario, as the Orange Lodge controlled much of the province's government. The Ontario Catholic school boards were a quid pro quo for Protestant school boards in Quebec. Well into the 1960's (Protestant) religious education was part of the public school curriculum in Ontario. Jews and other religious minorities were excused from these classes.

What happened in the 1980's was not the creation of Catholic boards, but the extension of funding for secondary schools to those boards. 

Quebec and Newfoundland have now changed from religious-based funding. Given that Catholics are no longer a persecuted minority, it's probably time to abandon the discriminatory practice of funding religious schools for just one group.