The original conflict between the Catholics and Protestants in Ireland was not truly a matter of religion — it was a matter of social class.
Put quite briefly, the majority of the population in Ireland, post 1000 A. D., was Catholic. They never underwent the church reform that England did in the 1500s. Thus, by the 1600s, England = Anglican (Protestant), and Ireland = Catholic.
When England began to establish plantations in Ireland and establish themselves as the ruling class, they often did it in a relatively unpleasant and domineering fashion, making themselves unpopular with their new subjects in the manner of America and India.
Hostility arouse between Catholics and Protestants in this way not because the religions themselves bore marked differences, but because these denominations were attached to two very different classes. Intermarriages were frowned upon, not for spiritual reasons, but because the Protestant was marrying below their class.