The Church in Ireland has always had a unique connection with the people. One has to remember/discover that pre-1100AD there existed the concept of "Celtic Christianity", which while not in any way a breakoff from Rome, was somewhat of a sub-set of Christianity that had it's own way of doing things, and it's base was Ireland. The elites of Ireland and the Church were closely allied.
In the 1600s as the Irish elites were more and more stripped of their powers, the English Protestants began to treat the Irish not as Europeans as such, but as "natives" in what would be a forerunner to further Colonisation in the New World. The goal of the English in Ireland was not to integrate the Irish and convert them, but slowly push them out. This is when and where the phrase "to Hell or to Connaught" comes from (Connaught being Ireland's most western province). The English in the 1600 already were pretty established in Leinster (the east) began to try and push in to Munster (south) and Ulster (north). They weren't too successful in the south, but their colonisation in the North was obliviously very "successful" as they removed Irish Catholics and replaced them with Protestant Scots.
So long story short, The Irish never took to Protestantism because the Catholic Church had always been "pro-Irish" while Protestantism was seen as Anti-Irish, the religion of the people who wanted to destroy the Irish and take their land. In Leinster there was some conversion, but really only amongst groups who were deemed Anglo-Irish/willing to submit to the idea of the forming "British" identity.