Islamic issues that trigger warfare

I have no doubt that most Muslims are good people. However, the problem that I have with Islam is that it IS political. Many of the issues present are of the type that war is waged over. For example, Islam specifies a foreign policy of when to wage war and when to make or break cease-fires. (Jihad is only part of this issue.) Economic policy is specified as well as exemptions from military service. These are only some examples of where Islam has the power of a modern nation-state. This is causing problems of loyalty within the Islamic world as loyalty to Islam can be in direct conflict with loyalty to the government where you live. Throughout history, resolution of these types of issues has triggered countless wars. For example:

One of the two major issues decided by the U.S. Civil War was loyalty to the state is NOT above the federal government. Most southerners were and are good people. (I was born in New Orleans) Resolution of the two issues of slavery and loyalty made the U.S. Civil War worth fighting and all of the loss of life that war causes. Islam has many more than just two of these types of issues. These issues are a major part of the reason why so much violence and warfare is present where Islam comes into contact with the world and within the Islamic world itself.

I consider these issues to be cultural in nature, much in the same way as southern loyalty to the state over the federal government. And like the South, the best future for mankind is that Islam does not win regarding these issues.