Two reasons. One was the idea of "Empire" had taken hold. We got over it.
The second was that the Empire of Japan was eying the Philippines and would have taken over.
When they did, during WWII, there was a mass slaughter of Filipinos.
Which was why Wendell Fertig had no trouble organizing "United States Forces in the Philippines" which gave the Japanese fits.
As far as the Japanese problem goes, wouldn’t placing the Philippines under a American protectorate have solved that problem just as effectively?