To claim that religious differences is a root cause of tension in the Middle East is to ignore much of what’s going on in the region today.
Are religious differences irrelevant? Not a chance.
ISIS wants to bring about an apocalyptic clash of civilizations. The heart of the Israeli/Palestinian conflict lies in primordial, irreconcilable differences between two groups. Sunni and Shiah Muslims are locked in a sectarian battle to the death.
We've heard these sentiments before, but are they true?
The more one studies the Middle East and its interweaving political disputes, the more apparent it becomes that differences often have more to do with economics, territory, and regional power grabs than with 1400-year-old theology.
Let’s start with ISIS, who continue to dominate news headlines, presidential debates, and Google search trends. While the group is quick to stress their religiosity (something which Western media outlets are more than happy to repeat, largely unchallenged), it’s important to ask how indicative ISIS is of the larger Muslim umma, or community.
The answer? Not very.
ISIS’s interpretation of Islam is largely grounded in the Quran, but one which the vast majority of Muslims reject. It’s a bit like Jews and Christians ignoring the sections of Leviticus which ban seafood, wearing clothing made of more than one kind of cloth, or working on the Sabbath. Nobody but the ultra-orthodox would question their religious devotion.
Most Muslims have no problem —and no cognitive dissonance— denouncing the actions of ISIS and remaining devout, practicing Muslims.
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The Israeli/Palestinian conflict is another arena where Western pundits are quick to frame the dispute as an "age-old" clash of civilizations, an intractable ethnic conflict. But this isn't accurate either. The debate is a geographic and political dispute more than a religious conflict, with two sides laying claim to the same parcel of land. David Ben-Gurion, Israel's first prime minister, is quoted as saying that “We and they want the same thing. We both want Palestine." 
The conflict has also gone through different stages, which point to it being a nuanced conflict with specific triggers and stages rather than one long period of sustained violence.
The chart above shows the variation in the death toll since late 2000. What's the cause for the variation? What was happening during the high and low points of this chart? What political decisions were being made? The answers to these questions would give us a better understanding of the dispute, and disprove the idea that it's an age-old vituperative conflict with no solution.
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The last idea, that Sunni and Shia Muslims have irreconcilable differences, is also one which is not well-founded in reality. This video from Al Jazeera makes the case well.
The current chaos in the Middle East "is "about power, not piety. It's a recent phenomenon, not an ancient one — we're talking 40 years, not 14 centuries."
Many media outlets looked at Saudi Arabia executing the Shia cleric Nimr al-Nimr and saw it as an example of renewed sectarian tensions, since Saudi Arabia is a Sunni country. But when the Iranian government denounced the killing and the Saudi embassy in Tehran was attacked, that was less a centuries-old conflict playing out than a geopolitical rivalry: for years, Iran and Saudi Arabia have had a tense relationship, with both countries vying to be dominant regional powers. In Syria, Saudi Arabia supports Suuni fighters, while Iran backs the Assad regime, part of the Alawi Islamic sect, which follows a branch of Twelver Shiism. In this context, however, such regional conflicts become less about religious differences and more closely resemble old fashioned proxy wars.
If all this sounds complicated, know that entire theses and books have been written on the subject, and this column is primarily designed to make you think about the nuances of the soundbites we hear in the media. Academics, journalists, and indeed anyone who wants to be informed about the situation must shrug off simplistic models of the world and see the specifics.
 Dowty, Alan (2013-08-26). Israel / Palestine (p. 82). Wiley. Kindle Edition.