It hasn’t really been a religious thing for a long time. It was stronger in Quebec while the Catholic church still had a firm hold on the province, but since then the Quebecois have gone secular with a vengeance. Any remaining suspicion of The Other is mostly political/linguistic. I don’t know for sure, but I suspect that anti-Catholic feelings in Ontario a century or so ago were as much anti-Irish as anti-French.
I don’t know if francophones ever used the term “limey” much. If they refer to les anglais, these days it usually means anglophones rather than English nationals.
There are bigots everywhere, but I haven’t heard “frog” used much lately. I have noticed a couple of instances where Americans use the term in a nudge-nudge attempt to ingratiate themselves to anglophone Canadians, on the assumption that the two solitudes are still at each other’s throats.
That’s probably the biggest source of Protestant/Catholic friction in Ontario today. Other religions are not always happy that Catholic schools are funded by the province while their own religious schools aren’t, but there are good historical reasons for the status quo. A proposal to extend public funding to other faith-based schools may have cost the Conservatives the 2007 provincial election.