Puerto Rico had been owned by the United States since the US took it during the Spanish-American War in 1898. It is part of the US. There have been multiple votes asking if they want to become an official state of the US. Other countries don’t get the choice to become US states. https://en.m.wikipedia.org/wiki/Territories_of_the_United_States#Incorporated_vs._unincorporated_territories
Puerto Rico is not autonomous. In Puerto Rico v. Sanchez Valle, the US Supreme Court found that sovereignty of Puerto Rico ultimately resides in the United States Congress. The US Congress can pass a law for Puerto Rico and there is nothing anyone in the Puerto Rican government can do about it. US Congress has ultimate control over Puerto Rico (see https://en.wikipedia.org/wiki/PROMESA as an example). That isn’t autonomous.
“If Congress chose to alter Puerto Rico’s political status, it could do so through statute regardless of whether a plebiscite were held or what sentiment such a vote revealed.” Political Status of Puerto Rico: Brief Background and Recent Developments for Congress (https://crsreports.congress.gov/product/pdf/R/R44721/7)