Actually it's not clear at all from either the CAA or Monarch websites.
It seems that Monarch flight-only bookings made in the UK are covered by ATOL (contrary to what the CAA site above suggests about flight-only not being covered). Having checked previous flight-only bookings with Monarch, an email is simply attached to the confirmation with the requisite ATOL certificate and in the bottom right hand corner of the certificate it states "Flight-only sale". The certificate has the names of the passengers, the dates and the flights covered, the amount of money protected (i.e. the total amount paid) and the booking locator. It specifically excludes any car hire or hotel accommodation booked at the same time. The issuer is "First Aviation", ATOL number 4888.
I assume that a holiday booking may qualify for a different type of ATOL certificate that may cover other items.