— Some Alawite (Shi'a) generals and officers defected from the Syrian army at the beggining of the uprising and joined the Free Syrian Army.
— The Sunni bourgeoisie in Damascus is not fightng Assad.
— The main force which has been fighting ISIS on the ground is a Kurdish one. The Kurds are Sunnis and ISIS fighters are Sunnis, too.
— Many Syrian Sunnis who have been displaced because of the war have fled to "Shiite" areas. They haven't been killing each other.
— The rest is geopolitics. Example: The Northern Alliance in Afghanista, although it included some Shiites, was mainly led by a Sunni-Tajik, Ahmed Shah Masoud. The Aliance was supported by Iran, among others such as Pakistan and the US. Masoud was assassinated by Taliban, a Sunni organisation.