You will be flying "back" to Athens anyway, especially when heading to Croatia from Santorini, whether your plane touches down in Athens or not. Changing planes is a necessity, since there isn't a great deal of traffic between Sicily or Croatia and Santorini. Hard to advise you how to go about it without knowing details of your trip (not even when you will be travelling) but it may make more sense to see Croatia/Sicily/any other place before Santorini.
From 6/1 to 9/30 there are several charter flights from Santorini to major European cities. For example, it is possible to fly from Ljubljana to Santorini and vice versa on Fridays for 299 EUR.
Also, from July to September, Easyjet flies from Santorini to Rome and Milan at least three times a day. In summer months Rome and Milan are connected to Dubrovnik and several other places on the Croatian coast (I'm not sure, but maybe also Zadar and Pula).Edited: 27 September 2010, 09:35
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