What military advantages did the Filipino insurgents have?
The Filipinos who were fighting against the United States did not have much in the way of advantages. They were never really anywhere near to being able to defeat the US in the way that the Vietnamese did decades later.
The Filipinos did have some of the usual advantages that freedom fighters have. They were able to move around the countryside with support from most Filipinos. They were able to melt into local populations and avoid being caught by the Americans. They were able to use their superior knowledge of the geography to hide.
However, these were all rather negative kinds of "advantages." They were enough to allow the Filipinos to kill many Americans, but not enough for them to come anywhere near to winning.