To say that we helped the Philippines become free from Spain is something of a misstatement. The Filipinos’ reaction was determined by the fact that we did not help them become free in the way that they wanted to be free.
If we say we helped a country become free, it sounds as if we have helped that country become independent. This is not what happened, at least not in the short term, with the Philippines. In the Spanish-American War, we defeated Spain and drove them out of the Philippines. However, we did not then allow Filipino independence. Instead, we took the Philippines as our own territory.
This is what determined the Filipino reaction. Filipinos had assumed that they would be free once we defeated Spain. When this did not occur, many of them became very angry. This led to a rebellion against American rule. The rebellion lasted just over three years and it is estimated that hundreds of thousands of Filipinos died as a result.
So, the brief answer is that the Filipinos rebelled against the US, but we have to add to that the idea that the US had not truly freed them from Spain.