Well, basically, the king was at odds with Parliament, he was a Protestant, but his wife was Catholic, and the King strongly believed in the return to the 'King as Deity' form of ruling. The King had to call parliament to raise money to go to War, that had been the way of things for about 200 years, but Parliament did not always agree with the King, so he was loathe to call sessions unless vital.
Parliament, however, angry at the King for taking a Catholic wife worked actively against them, effectively co-ercing the king to arrest and execute one of his own Lords (who happened to be in Northern Ireland). To cut things short, Parliaments dithering in giving the King money to defend against the Catholic Armies rampaging across Europe, coupled with NI's Catholic populations own fear of oppression (Aided and egged on by people sent by the Vatican) rose in rebellion. The official start of the War was the Slaughter and drowning of Protestants by Catholics near the River where the Orangemen now march, over 500 years ago. That's one of the official versions, though I suspect the whole truth goes much much farther.
Basically it was scared people being scared. I'll see if I can find you a link.
Edit :
http://www.globalexchange.org/countries/europe/ireland/historytimeline.htmlNote : This is a very contentious issue, I severely doubt you will find two people or even 2 articles that agree entirely on the causes
