Sunnis believe that we know the succession of Mohammed therefore religious leaders should function in government.
Shiites believe that the rightful successor to Mohamemd is yet to come and therefore no religious leader should sit in a positon of government power. This is why Shiite leaders in Iraq do not participate in Parliament.
But this Shiite position broke down in Iran when Khomeini took over in 1979. He not only thought religious leaders should be allowed to govern, he considered it mandatory.
While they have a theological disagreement the Sunnis and Shiites have been able to work together since the beginning of the Iranian Revolution. Arafat was a Sunni and trained the early Iranian Revolutionary Guard which is largely Shiite. The two groups also worked together to overthrow the Shah.
Those who claim that Sunnis and Shias can not work togther ignore the reality on the ground.
Info above paraphrased from “Understanding Iran” by Michale Ledeen written int the Hillsdale College – Imprimis.