Because Philippines has no National Government that time. Only local governments called Sultanato or Barangay so that they easily colonized us.
Because during that time, Philippines dont have a strong government to fought against the Spaniards. and the people were weak that they cant even fight for their rights in their land. and Spaniards like the Portuguese were very powerful that time, they are very advance especially when it comes to thier weapon! :) hope it help you! 
well during that time their was no education and all the the barangays before was not yet united. so what miguel lopez did was he went to the other barangays was made friends with others sultans and rahas and fought other barangays and that's how we were colonized by spaniards. the only provinces spaiin wasn't a bill to conquer was mindanao and cordillera.