The method, strictly speaking, was conquest, but not because of Protestantism. English adventurers first came to Ireland in AD 1169, under "Strongbow", the Earl of Pembroke. He was aiding the dispossesed lord of Leinster, which began a rather shameful episode of Anglo-Irish relations not ended to this day. Protestants did not come to Ireland until the 1530s, when King Henry VIII of England declared the Act of Supremacy in 1534, the declaration of English Protestant secession from the Church of Rome. From that point on English warfare against the Irish became by definition Protestant warfare against Irish Catholics.
By 1586 the Plantation System was in full swing, in which land was only owned by English and Scottish settlers, not the Irish. The Protestants could rent to Irish, but the Irish were no longer allowed to own land in the area of Ulster, in the north, and this spread to a large extent into the rest of the country. The most brutal phase of English warfare in Ireland occured under Oliver Cromwell, beginning in 1649.
On 11 July, 1689, forces under the deposed king of England (and Scotland and Ireland) James II and William of Orange, the new English monarch, met in the Battle of the Boyne. Oddly enough, though this is usually viewed in Ireland as a Protestant-Catholic struggle, since William's major political ally was the contemporary Pope. The victory by William ushered in an era of vague promises of fair treatment to the Irish, which were of course ignored by the victorious English leadership. These condition led to what is termed the Protestant Ascendancy, where in the 18th century Irish land ownership was reduced to 14% of land in Ireland. After 1704 Irish could not buy land, and all Irish held land had to be inherited by all sons, thus reducing Irish landholdings eventually to only small plots of land.
Essentially, Ireland was left a land ruled by Anglican lords, worked by Scots-Irish (ie, Scots who moved to Ireland) Calvinists, with the Irish Catholics reduced to poverty. This, of course, led to the conditions which resulted in the Potato Famine, the flight from Ireland of a vast percentage of its population, and eventually the rise of revolutionary movements. The revolution against England which began in the 18th century and has continued on to this day was, ironically, started by Wolfe Tone, a Protestant of English descent. Throughout the various Fenian uprisings and through the 1916 Rebellion and the Anglo-Irish War many of the leaders and soldiers fighting for Irish independence were Protestant. The only area of extreme Protestant-Catholic antipathy has been in Northern Ireland, an area containing part of Ulster (six counties) which since the Plantation days has been ruled ruthlessly by the small Anglican minority, who pit the working class Presbyterians and Catholics against one another.
It's important to remember that the real problem was never one of religion, but political oppression of the native population of a Celtic country by the invasion of a different ethnic group, the Anglo-Saxons. Although much of the conflict through the centuries has been couched in religious terminology, it has been economic oppression that has always been the main issue.