a Shia elected to lead a majority Sunni country or vice versa. As a matter of fact, everyone worries that the Syrian civil war will spark a wider Sunni-Shia conflict in the Middle East. To say that Sunnis and Shia "just attend different churches" ignores reality in the Middle East. To me they 'just attend different churches' but that obviously is not how too many who live in the Middle East see it.
In general, Americans do not consider religion as a great dividing issue. For the most part we don't care what you do on Sunday morning (or whenever your worship happens to be) or if you sleep in. That is not true in much of the rest of the world. For instance, Protestants and Catholics "just attend different churches" but that 'difference' was quite sufficient to lead to much violence in Northern Ireland and elsewhere in the past century.)
Rather than focusing on religion, Americans are raised to understand that race is the 'big divide' that has to be surmounted. Some Americans will not vote for someone of a different race - not as true now as 50 years ago, but still true for many. My sense is that the Sunni-Shia split is the 'big divide' in many Middle Eastern countries. The split doesn't seem like a reason for fighting to me, but neither did the split between Catholics and Protestants in Northern Ireland and there was plenty fighting there, too. (Oddly, Muslims must have wondered what Catholics and Protestants were fighting about since they are all Christians.)
Obviously, a Catholic or a Black can be a president of the US. (Heck even a Mormon had a shot at it.) Both have happened. It is not as obvious, to me anyway, that a Sunni can get elected president in a majority Shia country or a Shia elected president in a majority Sunni country. One day that will be possible just like an African-American could not have been elected here 50 years ago but it has happened.) I suspect that Assad doubts (to put it mildly) that he could be elected president in Syria. If he wants to retain power, force is his only option. I hope I am wrong and I am sure that one day I will be, because Syrians will learn that 'going to a different church' is not a valid reason not to vote for someone. As of today, however, I think Assad knows he could not get elected fairly.
I agree that differences in religion are different than those in terms of race, but in terms of its potential to spark violence the difference that makes someone an 'other' is in the eye of the beholder. To an American race is a much bigger 'deal' than religion. That is not true everywhere. The real tragedy is that whatever differences there are between humans some idiots will find that 'difference' (whether is is race, religion, gender, nationality, sexual orientation, etc.) a reason to decide that that person is an "other" which they feel justifies using violence.