The think with the territories of the Spanish-American War was that the United States went in with the original intent of kicking the Spanish out of Cuba, as such there were interests who were focused on Cuba; Puerto Rico was basically just territory gained and not a place anyone really cared about to the same degree as Cuba, hence why it was just annexed as a territory without anyone really saying anything about it.
Additionally, while the Teller Amendment was created and supported by a large amount of disparate groups, a good part of it was because many in Congress did'nt want to annex a place with such a large Catholic and Black population (Cuba at the time having a population of 1.57 million), especially since its sheer size, history and proximity would demand it become a State relatively soon after any annexation; Puerto Rico on the other hand, while predominantly Catholic and having a large non-white population (though importantly, unlike Cuba, a good portion of this was people of Mixed-Race, as opposed to just Blacks), had a smaller population (around 953,000) and was in a position that Statehood was not something that would have to be given immediately.