Boko Haram says hi. Anyways the real trouble is how Islam is considered not just a religion in a lot of the muslim world but also a political document. There is often no separation between the two perspectives at all. The Koran is enshrined in many constitutions as the guiding source of all law and morality. The same could be said about christianity and the Bible...about 300 years ago.
I am not religious, but I am not atheist either. I take the wishy-washy agnostic route. Which is why I think secularism is the best option. Religion should have no place in law and governance. The Renaissance and the Industrial Revolution gradually pushed aside religion from the central position of material power it occupied for centuries in the "west". There's few muslim majority countries where the same happened. Turkey is probably the most salient example. And regional rivalry is causing a resurgence of religious tribalism as the most important factor, not nationality (i.e sunni vs shia, Turkey has and continues to align itself with Saudi Arabia/Qatar/etc..., the conflict in Syria is a microcosm of the proxy cold war being fought for dominance of the region). Kemal Ataturk would be sad. You make Ataturk sad, Cicero.