Catholics and Protestants manage to co-exist in the south without killing each other and I don't suppose the IRA and their cohorts bothered about whether they were killing and maiming Catholics or Protestants, Jews or Muslims, Hindus or Buddhists when they planted bombs in Manchester, Birmingham or London. The people they did want to kill, maim or bankrupt were British, pure and simple.
A few years ago two Manchester men were working for a local company that had been set up by Irish immigrants in the '60s. It has an Irish name with offices in the UK and Ireland, yet when they were in Southern Ireland on a job they had to park up for the night near a small town. They went and had a couple of pints and a meal in a pub and while there they were approached by a local man who told them that Englishmen weren't welcome there and had better move on as something unpleasant might happen to them. They spoke to the local Gardai who said that they'd been given good advice. The fact both men were Catholics, in fact I'd been at primary school with one of them, was neither here nor there. Religion is an accident of birth and history.
What we do have is people who manipulate religion and the people who practice it. Religion is simply the lowest common denominator. Power is more important. The people who grew up with the power were those with the influence, and cronyism and nepotism ruled in Northern Ireland. I would say that this, more than religion, per se, is what brought about the new "Troubles". If you are in a position of power in a sectarian society then you will make sure your friends and family benefit before others. If you are not in that circle then you may object and if you think your concerns are not being addressed you may take more direct or violent action. If you have people who will supply you with a rallying call and the means of taking action with weapons/rocks/explosive.
What we are seeing now in Iraq is fuelled by al-Maliki's lack of inclusion of other groups. Forget Sunni and Shia, instead think disposessed and powerful; poor and wealthy; excluded and included. In other words, the have-nots and the haves.