I have been wondering about this too, because the credit card charges they add onto the payment are quite high. I found this:-
"Book a package holiday through a travel agent or tour operator and you’ll be protected by ABTA or ATOL should the company go bust. But if you purchase the flight, hotel or car hire separately through a travel agent, tour operator or website, you won’t have the ABTA/ATOL safety net as they only protect package deals." Plus, I suppose, you have your travel insurance too. I think I'm going to pay the balance of my Thomson holiday on my debit card....