As Mr V indicates, no flights booked directly with an airline are ever protected by ATOL.
However you have exactly the same statutory rights, with regard to things like delays and cancellations, whenever you fly from an EU airport, even if the airline is based outside of the EU. (You also have the same rights outside of the EU if the airline is based within the EU):
http://ec.europa.eu/transport/passengers/air/d oc/2008_apr_leaflet/apr_leaflet_en.pdf
Flight operators serving Mytilini International Airport are listed here:
http://en.wikipedia.org/wiki/Mytilene_Internat ional_Airport
It's unlikely that the 'seasonal' flights will be operating when you wish to travel, so you're basically restricted to using Aegean Airlines, Athens Airways or Olympic Airlines out of Athens. (If you book with BA you'll end up on one of those flights anyway).
Your options for travel to Athens are listed here:
http://en.wikipedia.org/wiki/Athens_Internatio nal_Airport
Since Aegean Airlines operate out of Stansted it might be worth checking their fares to Mytilini (via Athens):
http://www.aegeanair.com/
Olympic Airlines operate to Athens from Heathrow, Gatwick and Manchester, so their through fares to Mytilini might also be worth checking:
http://www.olympicairlines.com/
For budget flights to Athens (from Gatwick, luton or Manchester) try easyJet:
15:43 Fri 05th Jun 2009