jcaron mentioned this interesting Ryanair webpage that gives some reasons airlines may want to forbid their customers from using travel agents to book their flight tickets: customers may overpay, agents may not communicate the proper passenger information to the airline and agents may violate the airline ToS by checking in on behalf of the passenger.
Quoting their webpage (formatting is mine):
- [Third-party travel agents] make their profits by adding their own commissions to Ryanair flights and products, which means customers who book through them often pay more than customers who book directly with Ryanair.
- Some third-party travel agents often do not pass on to us your personal contact and / or payment details, which means we cannot contact you with important updates of your booking or process refunds directly to you.
- [Some third-party travel agents] may also complete the Ryanair check-in process on behalf of their customers in breach of our General Terms and Conditions of Carriage.
Also, from flyertalk.com that Gray Taylor pointed me to, some travel agents encourage behavior that goes against the airline ToS such as hidden city itineraries. E.g., on Kiwi:
