Islam has a number of structural problems that are the source of open conflict and warfare. A large part of the problem is that Islam IS political. Islam has an economic system. Islam IS a legal system complete with jurisprudence that goes back 1400 years. Islam has a foreign policy. Islam was designed as a nation-state long before they become common. This alone causes all kinds of problems as loyalty to Islam over ANY government is one of the issues that wars are fought over. (One of the two main issues that triggered the U.S. Civil war was loyalty to the state over the Federal government.)
Please note the number of medieval concepts. Such as the reward for jihad being booty. (Which was how armies were paid) Or stoning people to death. In fact, death is a common penalty which demonstrates another fact of the ancient world. Life was cheap. Islam has great difficulty evolving because it is GOD's word. It can't be changed as it is already perfect. Modern times has placed great strain upon many of it's fundamental concepts. Political Islam has to go and it is fighting organized warfare to prevent this. (I compare this to the good southerners who fought for slavery, or the good Japanese or good Germans who fought for the axis powers in World War II. They are good people who will fight for their way of life.)
Personally, I see the Koran as having been very poorly written. It is organized by the size of the phrases, which is a very simple and disorganized way to group ideas. If God had really supplied this information to us, I think that he would have presented it a hell of a lot better. Not to mention a little more compassionate.