Filipinos did not exactly rebel against American intervention. They did not rebel when the United States fought against Spain during the Spanish-American War. Instead, they rebelled when the US decided not to allow the Philippines to become independent but, instead, to keep it as a US colony. They rebelled because they wanted to be independent.
Up until the Spanish-American War, the Philippines had been a colony of Spain. Some Filipinos started a rebellion in 1896, hoping to throw off Spanish rule. The rebellion fizzled, but then reignited when US forces came to the Philippines to fight Spain. At that point, the Filipinos welcomed the US as allies in their struggle against Spain. After the Spanish had been almost completely defeated, Emilio Aguinaldo, the leader of the rebellion, declared the Philippines to be an independent country. However, the US did not recognize Filipino independence and fighting broke out between the Filipinos and the Americans.
The Filipinos who fought did so because they wanted to be independent. They did not want to trade one colonial ruler (Spain) for another (the US). This is the cause of the Filipino war with the US.