So does that mean Trump will pull U.S. Marines out of Okinawa and the U.S. Navy ships out of Japan?
No, it means that Japan will pay more to sustain our presence there. It is called burden-sharing. The US has been paying the vast bulk of the costs of defending the Free World, both in blood and treasure. We are going broke doing it.
FYI: The Japanese on Okinawa would like to see the US military out and have for a long time.
The US has defended Japan for a number of reasons. First, we do not want to see a re-militarization of Japan especially a nuclear armed one. Second, we helped insert Article 9 into the Japanese constitution, which the state formally renounces the sovereign right of belligerency and aims at an international peace based on justice and order. The article also states that, to accomplish these aims, armed forces with war potential will not be maintained, although Japan maintains de facto armed forces, referred to as the Japan Self-Defense Forces which may have originally been thought of as something akin to what Mahatma Gandhi called the Shanti Sena (soldiers of peace) or a collective security police (peacekeeping) force operating under the United Nations.
In July 2014, instead of using Article 96 of the Japanese Constitution to amend the Constitution, the Japanese government approved a reinterpretation which gave more powers to its Self-Defense forces, allowing them to defend other allies in case of war being declared upon them, despite concerns and disapproval from mainland China and South Korea, whereas the United States of America supported the move. This change is considered illegitimate by some Japanese parties and Japanese citizens since the prime minister circumvented Japan's constitutional amendment procedure.
In September 2015, the Japanese Diet made the reinterpretation official by enacting a series of laws that included that the Self-Defense Forces may provide material support to allies engaged in combat internationally. The justification is that by not defending/supporting an ally, it would weaken alliances and endanger Japan.