I think it is clear that flight-only cannot be covered ATOL.
However, it appears that a flight plus a car hire or a flight plus a hotel can. I have regularly booked an EZY flight and hired a Europcar car at the time of the initial booking apprently via the EZY website. However, as I understand, I am not buying a combined package because I am in fact dealing with EZY for the flight and Europcar for the car, albeit with a special "EZY" tarrif and apparently through the EZY website.
At first glance, it would seem the same structure might apply to Monarch but I have never tried. That is, unless maybe they have an in-house car-hire.