I think it's difficult for most of us in the West to understand the thinking and motivation behind religious extremism.  The extremists behind the Sunni/Shia conflict are essentially throwbacks to medieval religious thinking, where someone who doesn't follow your strict interpretation of your religion is instantly an apostate who can (and should) be killed straightaway.

Christianity went through the same sort of thing a few hundred years ago, and thousands upon thousands of people were imprisoned or killed outright.  Just in the last century, there was a rumbling of discontent about Jack Kennedy running for President - he was a Catholic, after all, and while nobody overtly said that all Catholics were apostates, there was no doubt that there was sectarian disapproval.

Of course, oil and international diplomacy play a big role in the Middle East, but we can't downplay the religious extremism that is at play here.