If Monarch sold a flight as part of a package, the Airline failure protection insurance will be covered by Monarch's bonded ATOL membership.
If Monarch sold a flight-only to the punter it will not be covered by Monarch's ATOL membership. If we are to be believed this is 90-95% of their flights.
BUT ... as Musician has said, the flight-only as sold by Monarch will probably have been sold through another operator with ATOL membership such as most UK Online Travel Agents (OTAs). I doubt many people are flying Monarch without the need for other products.
Provided a flight is sold with an accommodation or car hire booking by an ATOL member, it becomes a Flight-Plus booking (sometimes called a dynamic package). This will also benefit from ATOL airline failure protection insurance when bought through an ATOL member. At the OTA currently benefiting
from my services, of monarch bookings travelling the week before the administration, 99.9% were covered as flight-plus.
The 90-95% figure being banded around as "not covered by ATOL" is incorrect.