The Filipino rebellion against Spain was driven by many of the same things that had driven wars of independence in Spain's Latin American colonies. In other words, it was driven by the ideas of the Enlightenment.
Rebels like Jose Rizal wanted the government of Spain to be more responsive to the people and to be less harsh with things like taxation. They wanted the ilustrado class of Spaniards who were born in the Philippines to be allowed to participate in ruling the country. In other words, they wanted better, less harsh government and they wanted to have a say in ruling themselves.