I flew out of Santorini a few weeks ago and to be honest the airport is pretty poor for the CE traveller. There is no lounge and there can be long queues, although this tends to coincide with the charter flights leaving.

The terminal can get very busy as well. I found last time I travelled that it was worth heading up to the waiting area on the top floor before the flight - there is a small coffee shop and an outside terrace overlooking the apron which was marginally more pleasant than inside. Having said that I wouldn't want to spend any more time there than is neccessary.