Of course if you can make a booking elsewhere without a fee you'll do so.
But people, this is the way forward.
Airlines are cutting commissions because of decreasing income, travel agents have to charge the customer for the work they do.
Basically the fee of the airline on its website/via its reservation centre gives travel agents their possibility to charge a fee as well.
This fee is usually slightly higher than the fee the airline charges as they provide more service (search for lowest airline/fare, book your hotel etc etc). The more you use their service, the higher the fee. The more you do yourself (book via internet eg) the lower the fee.
Any agents not charging a fee or charging a very low fee will have difficulty to survive.