Not religion in the sense of theological belief, but religion in the sense of loyalty and belonging.

Christianity fractured in 1517 over the question of the extent of Papal authority and corruption. This led to centuries of power struggle as to who was superior: papal authority or civil authority? The UK eventually decided for civil authority in 1688 by installing a Parliament-respecting Protestant monarch rather than a Pope-respecting absolutist Catholic monarch. The ensuing fighting was ended at the Boyne in 1690. But it's still a battle the commemoration of which leads to fighting in the street in NI.

This led to a position of Catholic oppression by Protestants for centuries. Is this really a religious issue, or a self-perpetuating cycle of violence?

The parent's point is valid – although religion is the most obvious expression of social division, the roots are deeper. People don't erupt in open warfare due to differences in religion unless there are other issues – such as social injustice, or economic differentials, or so on.

Maybe it was a poorly chosen example, I though it was mainly a fight for independence. ETA (Basque) vs. Spain would probably be a better example.