Scotland, meanwhile had remained an independent Kingdom. In 1603, that changed when the King of Scotland inherited the Crown of England, and consequently the Crown of Ireland also. The subsequent 17th century was one of political upheaval, religious division and war. English colonialism in Ireland of the 16th century was extended by large-scale Scottish and English colonies in Ulster. Religious division heightened and the King in England came into conflict with parliament. A prime issue was, inter alia, over his policy of tolerance towards Catholicism. The resulting English Civil War or War of the Three Kingdoms led to a revolutionary republic in England. Ireland, largely Catholic was mainly loyal to the king. Following defeat to the parliaments army, large scale land distributions from loyalist Irish nobility to English commoners in the service of the parliamentary army created the beginnings a new Ascendancy class which over the next hundred years would obliterate the English (Hiberno-Norman) and Gaelic Irish nobility in Ireland. The new ruling class was Protestant and British, whilst the common people were largely Catholic and Irish. This theme would influence Irish politics for centuries to come. When the monarchy was restored in England, the king found it politically impossible to restore all the lands of former land-owners in Ireland. The "Glorious Revolution" of 1688 repeated similar themes: a Catholic king pushing for religious tolerance in opposition to a Protestant parliament in England. The king's army was defeated at the Battle of the Boyne and at the militarily crucial Battle of Aughrim in Ireland. Resistance held out, and a guarantee of religious tolerance was a cornerstone of the Treaty of Limerick. However, in the evolving political climate, the terms of Limerick were superseded, a new monarchy was installed, and the new Irish parliament was packed with the new elite which legislated increasing intolerant Penal Laws, which discommoded both Dissenters and Catholics.
Why did the King of England have issues with parliment in the 17th century?
his policy of tolerance towards Catholicism