After the Battle of the Boyne and such a treaty came to the table known as the Treaty of Limerick. This brought about a ruling in which Jacobites in Ireland were offered to leave to go to France or just pledge allegiance to King William, Catholics were treated well and all was fairly good. Unfortunately the English government weren't all too happy with this settlement and introduced the Penal Laws in an attempt to weaken the Catholic and Presbyterian following in Ireland, leaving Catholics and Presbyterians at a disadvantage to their Protestant neighbors. This isn't all the detail as to all the reasoning why it happened but it's all i can remember at the moment