500 under invoice makes sense if they just got the car in. As I understand it, automakers frequently give a sort of kickback to the dealership for purchasing cars, kind of as incentive for them to finance more autos to sell.
If the just got the car in, they probably have yet to make any payments on it... it's in their best interests to get it off their hands as quickly as possible, cause then they can just pocket the money Toyota has given them. This is especially true if this particular dealership has discovered that they can't sell the Matrix, but for whatever reason they're stuck with the ones they've gotten in (can't trade with other dealerships, ordered them before they realized it wasn't a hot seller, etc).
For my money, I'm willing to pay invoice, maybe slightly above on a new car, but I won't go over. The MSRP and sticker prices just seem way exhorbitant to me. 'Course, that may just be my frugal dustbowl roots talkin'