There are many places in which Muslims are defending their countries, and there are many places where Muslims are, like any other nation, defending their rights of liberation.
However, there are other groups that either use religion as a cover or bait (to bait recruiters, you all know how easy it is) to hide their own agenda and selfish needs. There are also groups who flat-out misunderstand their religion.
For me to decide on these places you mention, I have to inspect the conflict's history thoroughly, because it would be a big mistake to just judge with little information. Just because there are Muslims involved (1/6 of the world) doesn't mean Islam is the reason in it. Many of the conflicts, in Sudan for example, have reasons of tribal warfare, fighting over resources, as well as external hands playing into the scene.
If a government of an Islamic country ignores its religion's teachings and takes money from the people and preventing them the sweat of their brows, then it's not a religious issue anymore; for example.