They have no say in the matter, is the point. Because they aren’t a state, and aren’t allowed to become a state, taxing them would literally be applying one of the core justifications for US rebellion to Puerto Rico. Do we want Puerto Rico to revolt? Then we should either make them a state or not force them to pay federal taxes.
But unless we’re going to give them independence, we still have an obligation to protect and, to some extent, provide for them.