I'm an atheist (though I am legally a Sunni Muslim, according to my state records in Lebanon), but being an Arab I can give some input on the Shia-Sunni thing.
Basically, as in Christianity, there was a schism at some point and believers split into two groups, Sunnis and Shias. This happened after a succession dispute following the death of the fourth caliph (caliphs were the head rulers of the Muslim community in the past, though that evolved into them becoming more of just religious leaders, until the line of rulers was ended by the Ottoman empire in the early 20th century).
In the 1300+ years since the split, there has been a development of some religious differences, different laws and customs, and some separate holidays... But overall the differences are not that vast, frankly (to me, at least
). But the religious institutions are certainly separate, much like separate Christian denominations.
What's more interesting is that Shias are usually a minority in Muslim countries (Iran, Iraq and Bahrain being exceptions), and historically have often been adversely governed by Sunni rulers, and have often been poorer and less educated. So there is a strong awareness in the Shia community in general of the past and present situations, and there are certainly tensions between the two groups in some countries (not everywhere, though. Local factors matter a lot).
So.. yeah. In places with more extremist groups, those religious differences become amplified and the conflict increases. Similarly, when the demographics are not well aligned with the political representation, you get more tensions. That explains why the problem is more pronounced in some areas.