I usually do similar to Rosco: Expedia, hotels.com and similar sites, usually done through Quidco so there is a few quid back sometime in the future. I do all my China stuff for example that way with loads of windows open on various sites and book the best deal. I'm sure we all do the same.
Yes, if a wheel falls off you end up paying more. I needed to change an internal China flight recently from China Southern to China Eastern (or some such) for an hour or two later to allow for a change in another flight I had booked that is now arriving later. It ended up costing me £500 to take a leg out of an Expedia multi stop booking and add another single one way flight in that I wanted. Ouch! With a travel agent that would have cost less.
Wifey booked a flight to Europe to jolly with some pals in Belgium on some cheap arse website recently, that then cancelled the outgoing flight so the trip was kiboshed. Months later we are still fighting the credit card company to do a Section 75 refund as the airline only refunded the outgoing, and Bott & Co (who do our airline compo claims) have yet to get the compensation from them. It's a long and tedious process to save a few bob......
That said, I still did the odd holiday through Thomas Cook. We did a family holiday with Croatia with them not long ago. I'd not been before and didn't want to do the research - we just wanted an easy week or so in the sun. We booked a package with them, decent price, alright hotel, transfers, small details done at not much money and no thinking. Suited what we wanted to do. Maybe it was £100 more than I could have done it myself but time +/- money, etc., it's about the same.
In the past I've done trips to Florida with them. Prices were quite keen, car hire options were good (with no rip offs), hotels were keenly priced, but what I found useful is you were doing an £Xk trip, you can pay £Xk deposit, and drop in with £500 occasionally over a few months and before you know it, its paid and you didn't feel it.
Like Moby says, the ATOL protection (that is bringing all these people home) has a value, but people dont see it till they need it.
I'm sorry they are gone, but I dont think the government should have rescued them as some suggest. Yes it's a lot of jobs and capacity at Manchester Airport but the market will adapt. At the end of the day, an insolvent business is an insolvent business.