Indeed the marinas in Athens are expensive with prices comparable to many marinas in France but this is not to say that all marinas in Greece and the rest of the Med are very expensive. Look at our wiki Marinas - Greece
and elsewhere there. In general, marinas in Greece have a price structure that the price/day goes down the longer you stay.
As Kirk has pointed out there many wonderful anchorages where you can anchor for free. Also, in Greece most harbors, other then commercial marinas, charge a very nominal fee.
If you have any specific questions, not answered in the wiki, do not hesitate to contact me.
I am now with my sailboat in the island of Samos, Greece