You need a longer view of Philippine history.

The main factor in the US success is that the US displaced the Spanish/Catholic Church. The friars owned the majority of the estates in the Philippines - these lands were offered up to wealthy Filipinos in exchange for their support of US governance. As well, the US gave urban elite Filipinos the opportunity to participate in the new government.

These two moves deprived the insurgents of the support they would need to wage an effective rebellion against the US.

The war that was fought was shaped by this as much, if not more, than it was by the tactics or COIN strategy of the US Army.