The Muslim insurgency began in the early 1970s and the fighting has killed some 150,000 people as well as plunged large parts of the south into deep poverty.
Propaganda.
The people along the chain of islands called the "Sulu Highway" were ignored by the central government in Manila for years. They hiked up their own boots and built schools, hospitals, and other infrastructure. Suddenly, the central government wants to take charge. Amazingly, this coincided with the "War on Terror", and the US desire to have a footprint in the area. Of course, the Filipino's stand with their hand out and say, "I want to be your friend" as we hand over military equipment and money.
The end state is the Philippine Army walking into a village and telling the inhabitants to leave, for no reason other than they are "evil muslims". If they don't leave, they die when the Philippine Air Force bombs them.
Deep poverty? Many of the tribal people in that area don't want the western comforts. It's not poverty, it's their lifestyle.