As unsatisfying as the answer may be the answer really is that the 50-ish years of direct US rule and decades since of cultural and economic orbit were enough to put English into 2nd place behind Tagolog and its peers/cousins.

We can see why this would be the case too. Most native Filipino's only knew Spanish because they needed it to interact with their colonial government, or missionaries, or economic interests from Mexico or Spain herself. When that gets replaced by English suddenly you have greatly reduced incentive to continue to teach, or learn Spanish and plenty for English. While the US DID have motivations to make sure there wasn't another language out there that could bridge divides between the various native languages, Spanish had been the primary method of communication in the major revolts at the end of Spanish rule. While Aguinaldo and the rest had spoken, used, and written the early documents including their Declaration of Independence in Spanish.

So with the coming of new colonial rulers, decades of economic activity, new generations being taught in state run schools with controlled curriculum, the death of many of the leaders who spoke Spanish, and the growing cohesiveness of the islands populations Spanish didn't die out but didn't really grow.

And that is reflected even in the current Constitution from 1986. It names Filipino and English as the main languages, but does call for along with local translations, access to translations into both Arabic and Spanish.

So yes the US's heavy handed rule in the islands certainly took steps to imprint themselves as the new boss. That included using English wherever they could to supplant Spanish and Filipino. And yes especially as it relates to the insurgency in places like Mindanao the word Genocide has been thrown around but that's a very separate sticky issue. And yes Manila as the old heart of the Spanish govt and new seat of US rule was rocked by rebellion during the Philippine Insurrection, and later devastated in the 1945 battle. And even after independence the orbit of the Philippines around the US has continued to offer far more incentives to learn English over Spanish.