There are many reasons for this, and I would recommend the work done by Vicente Rafael on this topic. I particularly recommend the books Contracting Colonialism and The Promise of the Foreign.

A simple answer is that Spain did not colonize the Philippines in the same way they colonized territory in the Americas. Spaniards did not move to the archipelago in large numbers, and Spanish was not used heavily during the colonial era by Filipinos. In fact, as the colonial period moved on there was pretty strict segregation. In Manila, for example, the Spanish population lived inside Intramuros and was not allowed to mingle with the Filipinos. Marrying or even having relationships with Filipinos was discouraged (this even shows in the genetic makeup of the Philippines; most Filipinos have very, very little or no European background). So the language was probably not passed on through family very well since most people did not speak it fluently, and were not having families with native Spanish speakers either. The Spanish wished to avoid a situation where a mestizo class would lead an uprising against them.

In addition, it appears that the Spanish didn’t try to spread Spanish in part as a way to separate themselves socially from Filipinos. Classism, basically. Spaniards noted the few numbers of Filipinos who could read or write or even speak Spanish fluently, even by the end of the colonial period. Elite Filipinos did know Spanish, as they were educated in Spanish educational settings. But this appears to be a fairly small minority. It’s uncertain how many fluent speakers of Spanish there were (Spanish census data is a bit unreliable due to the methodology) during various points in the colonial period, but it never achieved anywhere near large enough numbers to succeed as a lingua franca. In fact, Filipino nationalists attempted to use it as a lingua franca, but ultimately it was a failure. Again, this lack of education system could possibly be seen as a defense against popular resistance (at least, in my opinion).

Now, the Americans also affected Spanish usage during their time as colonial power. English was immediately incorporated into the new education system that they were creating, and was required learning. Americans pushed English at the expense of Spanish, and over time the Spanish speakers dwindled. This was not helped by the fact that Tagalog became the new official language during the Commonwealth and afterwards. Spanish was finally removed of any status later, but it already had very, very few speakers by that point anyways. English has continued to be required in school in the Philippines to this day. It is a huge prestige language in the country. That being said, Tagalog and the other native languages are absolutely the primary languages above all else, though English does have a psychological allure for Filipinos. For more on these topics, again, Rafael is a great source, this time from a book called White Love and Other Events in Filipino History.