On larger islands, with more than one castle, defensive plans were drawn detailing which would shelter the people of specific villages. Castles were paid for out of the Public Fund of the Order. Sometimes an extraordinary tax was imposed on the islands residents which they were more than willing to pay. During the latter half of the 15th C with the order under decline, aid was infrequent or non existent from the Pope and the regents of the West who were constantly squabbling for power amongst themselves. The Venetians even traded with the Turks and didn't want to upset them. The Genovese were more helpful and enemies/rivals of the Venetians.
Although built by the Order, island residents were obliged to help in castle construction and maintenance. In addition to paid workers, they also used their own slaves and slaves of island residents if necessary. On the smaller islands defense was the responsibility of the islands leadership but always under Hospitaller supervision. To minimize surprise attacks, the Knights used an elaborate network of coast watchers, spies and informers particularly in Constantinople to be informed as to the state of readiness of the Ottoman navy. Sometimes they allowed the settlement of other islanders on Rhodes on coastal land under the stipulation, a coast watch would be kept.
There are many more castles in the Cyclades as well and these were mostly Norman, Frankish and Turkish in origin. Castles everywhere, since many are up high, in out of the way places with excellent views make a great hiking destination away from tour buses. Many more one can drive to such as Acro Corinth and then hike amongst what some have called 'the best fortified position in Europe'. Its certainly one of the best views in Greece.
There are of course many ther fortifications on Crete and other islands which you can read about in the individual island guides.