I've had the thought: after the American Revolutionary War and Irish rebellion, the British require settlers in Upper Canada to swear an oath of loyalty to the King/Queen, and specifically rejecting Popery. Irish Catholics are required to settle in Lower Canada and are "encouraged" to marry with Quebecois, thus assimilating them.
Meanwhile, Europe and/or Britain is wracked by another round of Catholic/Protestant conflicts in the 19th century. The British seek to populate British North America, but are fearful of Catholics.
When the Prairies are opened for settlement, farmland is allocated based on religion: Protestants receive the most fertile and accessible land, while Catholics receive less optimal land. High level civil service are tacitly restricted to Anglicans.
By 1900, the religious balance of Canada is as follows:
Quebec: 85% Catholic, 10% Anglican, 5% Presbyterian and other Protestants, some Jews
Ontario: 70% Anglican, 10% Presbyterian, 15% other Protestants (German and Scandinavian Lutherans, Dutch Reformists, a smattering of others), 5% Catholics (mostly underclass workers from Quebec)
Prairies & West: 60% Catholic, 15% Anglican, 15% other Protestants, 10% Russians, Jews, and Chinese thrown in
I've just turned Canada into a giant Northern Ireland!