The car is a 2003.
2003? 
I think you should try to get the dealer to fix it again for free, if you haven't already.
...and then sell it ASAP.
I should bring it in, but its so damned inconvienient to be without a car. I really wasn't impressed with the finish the first time.
...
The rust on the door sill is due to tiny stones and grit that get trapped around the plastic plate that is supposed to protect the paint from scuffing when getting into the car. Grit gets trapped under it and between it and the rubber door seal. Of course its the driver door and the rear door where the kids go in that have the worst. There is a tiny outline of rust visible when I remove the sill plate and clean up the area (which is not very often).
Just to follow up on this thread. I did take the car in the the dealer body shop. Toyota agreed to repair the rust on the door sills and the underside of the trunk lid (above the latch).
This time, after refinishing the door sill, they added a plastic overlay between the metal and the plastic sill cover. The body shop did a much nicer job on the inside trunk lid this time.
However they would not cover the rust bubble on the edge of the front hood.
