There is considerable debate over what role religion actually plays in the Norther Irish inter-community conflict among scholars of Irish history and politics, so any answer to this question is going to be taking something of a side in what is still very much a live debate. That said, here's my read on the situation. The inter-community animosity in Northern Ireland has, in the latter half of the 20th century through the present, been much more "tribal" than it is religious, per se. That is, the animosity between the Protestant and Catholic communities is based much more on in-group/out-group dynamics than it is on substantive disagreement over tenets of Christian faith. Few if any of those who participated in the Troubles understood themselves to be fighting for their interpretation of Christianity in the way that, say, fighters in 17th-century religious wars would have. It's much more, to my mind, about political agendas, social values, and tribalism than about actual religious doctrine, although Unionists do tend to fear the influence they suspect that Catholic doctrine would exert over the politics of a 32-county Repubic.

All of this is a complicated way of saying that religious belief alone doesn't count for much by way of making friends and enemies in Northern Ireland. It's much more about which group or "tribe" one belongs to (Catholic-Nationalist/Republican vs Protestant-Unionist/Loyalist). Essentially, religion serves as shorthand for political/tribal affiliation. As proof of concept I offer two facts: 1) Not all Ulster Protestants belong to the same denomination. Many are Church of England (Anglican), but a number of Presbyterian sects are also strongly represented. 2) If you're not Irish or of Irish descent, modern-day Northern Irish people, even those who feel strongly about sectarian politics, don't care much about you one way or the other. You're just a foreigner with no real stake in their fight. Now, if you walk up the Shankill wearing a tricolour T-Shirt or down the Falls waving the Union Jack, you'll get your ass kicked even if you're a Mongolian Hasidic Jew.

Hope that helps. A couple of methodological notes- Apologies for use of present tense. Your question has to do more with the social realities of the Northern Irish inter-community conflict than the actual historical events of the Troubles, and those realities are very much ongoing. I'm drawing from my research into the Troubles (I'm a PhD student at a major university writing my dissertation on the politics of Anglo-Irish counterterrorism strategy in Northern Ireland) and my experience traveling and talking to folks in Northern Ireland about their experiences and interpretations of the conflict.

For the best counterargument to the "conflict in Northern Ireland is essentially political, not religious" thesis which I admittedly take for granted, see Marcus Tanner's "Ireland's Holy Wars: The Struggle for a Nation's Soul 1500-2000" (2003)

Follow-up Question:

From my understanding, the troubles were more Irish vs. English that just happened to line-up wit Catholic vs. Protestant rather than a full-on religious war. Is this not so?