ATOL do not cover flight only bookings of any kind that are booked direct with an airline. From the CAA (who run the ATOL scheme) website...
Airlines are not included within the ATOL Scheme, so if you booked direct with an airline that has ceased trading you will not be covered.You may be comparing flights booked direct with an airline with the same flights to be booked through an ATOL holding agent or holiday company. £80 seems way too much for that though - Aegean Flights charge £2.50 for ATOL protection (remember Aegean are not an airline, Onur are the airline normally). Even having paid that, it's sketchy as to what you would do as the CAA in those cases would, if the airline went bust, direct you back to Aegean and would not listen to any claim under the ATOL scheme from you.
Complicated isn't it
