I'm pretty sure I recall FM 3-24 stating that "every" situation is different. The communist insurgency and the Muslim separatist movement in the Philippines have little to do with the war on terrorism and in this almost everything to do with poor governance. The CPP and NPA have remained isolated from external due to choice and geography, and while the Muslim separatist movement has some degree of international support, it is mostly moral and financial in character.

On the other hand, the threat we responded to were the terrorist groups in the Southern Philippines (JI and ASG), and at the time we responded they were relatively strong and their strength was growing. They were suppressed by a combination of aggressive security force operations and civil-military operations (CMO wouldn't have worked without the aggressive security measures), and equally important a great effort was made to separate the Muslim separatist movement from its illegimate brother the terrorist groups (ASG and JI), so we didn't artificially conflate the issues. Of course, like most things dealing with politics, social movements and conflicts (or more simply, people) there are gray areas, so you can point to exceptions where there were links.

Like every prolonged conflict, the character of it changes over time. For the most part the threat of Islamic radicalism in the Southern Philippines has been suppressed (not defeated), but the issues of separatism and communism remain and will remain until the government reforms "itself". IT isn't our role to reform their government, but as allies we can provide a helping hand if asked. It is important to note that the Southern Philippines could easily slip back into the dark days if "security forces" can't effectively apply pressure.

IMO the greatest threat of terrorism in the Philippines (outside of insurgents using terrorism as a tactic) is the growing Balik movement that can potentially be radicalized. The threat of Islamist based terrorism is not restricted to the Southern Philippines.

The JI has also been under a lot of pressure in the Indonesia by its security forces, so right now it appears the organization is having a hard time finding its balance; however, if that pressure if removed they'll reconstitute because the underlying driver has nothing to do with "good governance" and everything to do with radical ideology, and the desire to establish a caliphate. What most of us would call "good governance" they hate with a passion and it is the reason they're fighting. They don't have popular support and probably never will, but they have a cause they believe in, and the only way for those who oppose that cause to have an acceptable level of security is to conduct aggressive security operations to suppress the radicals. The basic rule applies here, the side that most effectively (means skillful application of force, not brute force) applies coercive force wins. There isn't a happy middle ground with these organizations that their opponents can negotiate, because their views are extreme, which is why we label them as extremists.

While there may be some similiarities or even parallels to Afghanistan, there are many more differences, which is why I cringe when I hear we should apply the Philippine model in Afghanistan. The Philippine model (if indeed it is effective) is only effective in the Philippines. The ideal Afghanistan model hasn't been developed yet, and when it is it will be based on the real dynamics in that region (not our politically correct view of the way it should be), not in the Philippines.

Long way of getting to your question, but in short the terrorists in the Southern Philippines were suppressed by effective security operations that were enabled through CMO. What we're talking about is warfare, and warfare has never been restricted to simply the application of violence, but the application of violence always plays a role.