From "Embracing Defeat" by John W Dower we can gather a few reasons. Remember that Okinawa was invaded by the US, and the population much reduced in the ensuing struggle. "Okinawa, under the draconian control of the United States, was shrouded in secrecy as the Americans built the strategically situated island into a major Cold War military base. Throughout the occupation, and indeed until 1955, no news reports or commentaries about Okinawa were published in the press.."

So it was a big Cold War base. Now remember that the islands north of Hokkaido were captured by the USSR. In 1952 the occupation was over and the Peace Treaty went into effect. From the same book.. "Although in the end the pace treaty would involve scores of nations, the Americans controlled the peacemaking process; and the exact price Japan would be called on to pay for incorporation into Pax Americana became apparent only bit by bit. Rearmament under the American "nuclear umbrella" was but one part of that price. The continued maintenance of US military bases and facilities through-out the country was another. Okinawa was excluded from the restoration of sovereignty (just as it had been excluded from the occupation reforms) and consigned as a major U.S. nuclear base to indefinite neocolonial control. Because the Soviet Union was not part of the peace settlement, it's disputed but defacto control over islands north of Hokkaido remained unresolved."

Not in the book, but pertinent to the final part of your question, Okinawa under US control was not popular, there were protests and riots, and a new treaty was signed, that still gave the US rights to the bases there.