At the time of the Spanish-American War, there were a number of different arguments that were made for granting Cuba its independence. Some of them include:
We do not want Cubans to become Americans. During this time period, Americans were typically quite racist. They did not want non-white Cubans becoming American citizens.
We do not want competition from Cuban sugar. If Cuba becomes part of the US, its sugar will compete with sugar from American states. By making Cuba independent we can protect the interests of domestic sugar producers.
Colonizing other countries is not the American way. The US was created by people who did not want to be a colony. Our country is founded on the idea of liberty and independence. It would be hypocritical and wrong to control another country that wants to be free.