Irish-Catholics and British-Protestants have always been at odds with each other but how did Religious differences play a role in the formation of countries and cultures in the British Isles.
Tensions -- and even open conflict -- between Catholics and Protestants was a feature of domestic British politics -- and not just British-Irish relations -- until the Glorious Revolution of the 17th Century. Essentially, a Roman Catholic King (James II) was forced from the throne by a coup-d'etat of sorts and replaced by William and Mary (Protestants), thus the Church of England was firmly established as the official state church. In Northern Ireland, of course, this conflict lasted much longer; for example, it wasn't until the 1820s that Catholics were even allowed a say in government in Northern Ireland. For a succinct summary of the role of religious/inter-communal conflict and the formation of the modern British state, you can see "The Making of the Modern British State" in Kesselman, Mark and Joel Krieger, European Politics in Transition (2009).