It was a struggle over nationhood or national identification in which religious affiliation came to play an ever more important part in the north. Ironically Protestants like Henry Grattan had been in the forefront of the first constitutional moves toward self-government (many Catholics paradoxically later preferring union with Britain in the hope of achieving full rights and breaking the political monopoly of Protestant landlords), while Wolfe Tone, considered the founder of Irish Republicanism, was himself a Protestant who had earlier identified with England's Whigs.
Much changed with Catholic Emancipation and the extension of the franchise in the 19th century. Gone were ideas of a Protestant-ruled island: most southern Protestants (a small minority) became resigned to majority rule as Home Rule became an ever likelier outcome after its adoption by Britain's Liberal Party in 1886. But it was a different matter in Ulster, where Protestants remained a majority after the 17th-century Plantation and later immigration from Scotland. British Conservatives quickly embraced northern Unionism as an ally against their Liberal rivals, sparking a UK-wide constitutional crisis as Home Rule made it into law in 1912-14, only to be deferred for the duration of WW1.
As we know, partition followed in 1921, with the six northeastern counties being retained under British sovereignty but governed by a Unionist-majority Northern Ireland parliament. Half a century of discrimination followed, deepening the religious divide and sparking the upheavals of 1968.
Nationalists and Republicans (many of the latter themselves deeply unmoved by religion and indeed sharing Protestants' desire to be free of Catholic Church influence in political life) maintained throughout that their respective campaigns were about nationhood, not religion, but the conflict developed ever more sectarian aspects in which some ultra-Unionist Loyalist armed groups took the lead but others followed with reprisals.
Ending the conflict took the form of recognising two "traditions" - an elegant but necessarily vague concept embracing political, religious and cultural dimensions. At the end it was both national and religious, and the tensions remain so. But the background was more political.