I've had the same experience, especially with making changes - places I've worked where we could arrange the travel, changes would be easy since we'd book flexible, make changes through the airline's web site and not pay fees, but with the travel agent we'd often have to call, so we couldn't easily make changes out of business hours (when we often needed to) and then we'd have to pay the agent a fee for the service of doing something we could have just done on the airline's web site ourselves.