I agree with Globaliser. It can also be a different experience depending on whether you are booking a "package" or flights & accommodation separately. Nowadays, I often find it cheaper to book directly with the airline concerned, than through a consolidator, and you usually escape the added booking fee!
I have not used a Travel Agent in over 10 years, and my wife and I go away at least once every year. During this time we have been on several "package" holidays, all booked online without any problems.
The recent double merger of the four biggest players in the UK package market threw in some interesting anomalies! Shortly, after the merger of Thomson and First Choice, it proved cheaper to book a long-haul package to a Jamaica destination through the Thomson site, using a First Choice flight, than it was chosing the exact same holiday directly through the First Choice site!
Your problems with Thomas Cook may be the result of the merger with Airtours, since their respective systems were not necessarily compatible and easy to migrate!
I do hope you try online again, and that your experience is more rewarding.
