Yes, in some cases. If you book a flight with an ATOL holder (either direct or through a travel agent) and you get an ATOL Certificate as soon as you make payment, your booking is protected if the ATOL holder fails and the ATOL holder is also obliged to offer a refund should the airline that you are booked with fail financially.
Remember though, if you are not ATOL protected and you book with a travel agent, make sure you receive your airline tickets as soon as you pay. That way, should the agency fail, the airline should honour your booking. In these circumstances you are not directly protected against the chance of the airline that you are booked with failing, so you should check whether any travel insurance that you have includes it, and, if not, consider taking out additional cover.