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The problem in nations like Syria isn't merely sectarian, but it's cultural. You have completely different cultures that want their government to do completely different things, and they don't generally consider themselves to be "one people" with the other cultures and are therefore unwilling to subjugate themselves to the desires of that other culture.
The Ottomans were smart enough to know this, which is why the area we now know as "Syria" was made up of several Eyalets in their empire. An eyelet essentially functioned as an independent nation, with its own government, laws, and cultural norms. Each was answerable to the Ottoman Sultan, and the local laws couldn't override the Sultans laws (much the same way that our state laws can't override federal laws), but each culture and region had their own eyelet operating in sync with their own cultural norms. Everybody got along fairly well because they didn't have cosmopolitans on the coast imposing their worldview on rural inlanders, Sunni's weren't imposing their religion on the Shia, Christians had representation, etc. Everyone got to live the way they wanted, in areas that accepted their own cultural norms, and the region was relatively peaceful as a result.
Then, after WW2, the Europeans came in, disbanded the Ottoman empire, and drew arbitrary lines that had little or no correlation to the actual peoples and cultures within those lands. Some people, like the Kurds, ended up with no representation or lands anywhere. Others, like the Sunni in Syria, ended up majority populations in lands run by a minority under cultural norms they never agreed to. The result has been a century of war.
This is what the middle east looked like BEFORE we redrew the maps to benefit the western powers. You'll notice that there is almost no correlation between these "natural borders" and the borders we see in the middle east today. The area we now know as "Syria" was carved out of the Eyalets of "Lebanon" (the tall skinny one along the coast), "Aleppo" (the one touching the coast just above Lebanon, and extending well into modern Turkey), "Syria" (the tall, skinny one just inland from Lebanon), and "Zor" (the large province inland from Lebanon and Aleppo). Those borders actually worked for everyone and kept the peace. Maybe the solution is to just admit that the Ottomans knew better than we did, and encourage the re-establishment of those older borders and nations. It the Europeans had simply granted nationhood to each of the eyalets in 1910, we wouldn't be having this conversation right now.
