Racism had a lot to do with it. When Hawaii joined the Union there was a sizeable white population to go with the local Pacific Islander population, which in itself was relatively small. In the Philippines, there were fewer American settlers and there was a massive, generally uneducated and in poverty, mostly Catholic, Filipino population. Bringing that into the Union would have created a nation that was 1/4 Filipino, and many Americans at the time were not prepared for that diversity. Bringing up the Filipino population to the American standard of living would have extremely difficult and expensive.