As the struggle for autonomy ensued, the main center of attraction was the disagreement between the Catholic and Protestants. As much as the major players in this struggle subscribed to various religious beliefs, their conflict had very little to do with their sectoral beliefs but had more to do with their socio-political sentiments. Land and policy confiscation was at play, which went as far as dispossessing Catholicsand the adoption of English Law in certain parts of Ireland.
Some Catholics remained, and these remnants wanted their concerns to be known. In light of this, there was serious resistance to the pro-protestant rules by the Catholic community. The Counter-Reformation was led and orchestrated by Jesuit Catholic Clergy, who were specially trained to lead the revolt. This is what brought about the perceptions that Irish Catholics were more native and that 
the Protestants were products of state policy. At this time, Catholicism was viewed as treason.
Existing penal laws against the Catholics and Presbyterians were renewed in the early 18th century. One of the many reasons was to reduce the opposition. They achieved this by relaxing penal laws against Presbyterians, which implied that Catholics were on their own. As much as it could have been challenging, the Catholic support for Jacobinism continued.
Sectarian conflicts never stopped after the Anglicans befriended the Presbyterians. In the late 18th century, the conflict now took the shape of having different communities fighting each other. From the looks at developments in the 19th century to date, the struggle continues. For a fact, modern Irish nationalism often view anti-Protestantism is more of a national issue than religious. This reinforces the fact that Anti-Catholic and Anti-protestant prejudice still exists in some parts of Ireland.
