As far as I can tell, the two big disadvantages are, as the previous poster mentioned, making changes to a web-travel ticket MAY not be as simple as dealing with the airline directly (I've had two instances where I've needed to, and in both cases Travelocity failed miserably, but YMMV); the second is that it is not always easy (or possible) to know exactly what booking class your ticket is being booked into. I remember asking an Expedia agent once what booking class a certain ticket was being booked into, and she looked and looked in her file and had no clue what I was talking about. Evenutally, a supervisor dug it up - so beware if you need qualifying miles!