I guess that AA
gives out net-fares to Expedia and similar websites - they just add on whatever they want to earn by selling the fligh and put that in their database.
Often enough that will lead to secondary vendors (in other words - not the airline) having better fares than the airline itself, because most airlines will only let you book their published fares through their own websites.
There aren't many nice things that airlines do to us travel agents these days, but net-fares are definately something nice... let's you play with the price and, often enough, either undercut the official price for an itinerary, or it'll let you make at least a bit more than with the normal published fares.
P.S.: Some of what I just wrote is only valid in markets, where airlines have not adopted the 0%-commission-model that they have, for example, in the US: in those markets, a net-fare will, essentially, always give the travel agency (and Expedia and similar are, effectively, travel agencies) a better income.