Religious differences certainly are one root of the problem; Sunnis and Shi'ites never should have been stuffed into the same artificial country. Imperialist idiocy is the other root...Sunnis and Shi'ites never should have been stuffed into the same artificial country. Who the hell made that decision, and when? The Brits after World War I? The French got Syria if I'm not mistaken.
I think one of the reasons Japan and Germany went so well was that the populations there were fairly homogenous. The Nazis drove out or exterminated minoritiy groups in their ridiculous effort to "purify" the German nation, and the Japanese were, well, Japanese. It's safe to say that many, many other factors came into play, but lack of extreme factional strife in the occupied territories certainly didn't hurt.