I'd say irishguy28 sums it up pretty well.

It's true that if you have the PNR your can usually do some basic things on your own. You can probably view your reservation and maybe select your seat(s). But, if anything happens that requires an actual change to your ticket before you get to the airport, you will be forced to deal with the travel agency that made the booking.

One thing that's become critical given the massive number of flight cancelations is notifications. When you book with a travel agency (traditional, corporate, or online), the airline will notify the agency of any schedule changes or cancelations for the tickets they "own". It is the responsibility of the travel agency to notify the traveler.

In that situation, the traveler must contact the travel agency to make any changes to the trip. While moondog may be lucky enough to have found a travel agency with excellent agents in his/her part of the world, I can assure you that the customer service folks at US sites like Expedia and Orbitz aren't typically very good. So, you'll be at the mercy of the ability of whoever happens to answer the phone when you call for help.

Disclosure: I once worked at a specialty travel agency call center. I started as a phone agent and moved into the Training Department. Many of the agents I trained were great. Some were good. And a small number were barely adequate. So, I really mean it when I say you're at the mercy of the ability of the person that answers when you call a travel agency for help.