Many frequent travellers here will tell you that booking directly with the airline, or through a reputable human/bricks and mortar travel agent is well worth the few extra bucks. Yes the online agencies can save you a bit in the short run, but they're never there to help you when things go wrong, and where they are, many of their agents are poorly trained. Going through a call centre or calling some random person in a foreign country is never going to work if yore at the airport and need a problem solved quickly.

For my leisure travel I book directly with the airline(s). For my business travel I book through a human travel agent who knows what I want and need. When I have a problem or a booking that needs changing, I call him, give him the details, and he calls me back within a few minutes to tell me that he has solved everything for me.