According to the service manual, that cover is under the carpet under the left side (driver's side) of the rear seat. (That's the main rear seat, not an optional 3rd row seat.) The seat has to come out to get at it.
I'm willing to bet that said cover isn't big enough to service the fuel filter, but I hope I'm wrong. It would be great if someone who has done this could post a reply. It looks to me like the only purpose for that cover is to allow you to disconnect a wiring harness prior to dropping the tank.
I'm kind of surprised that Toyota would put the filter inside the tank - they must not expect you to change it very often. There's no mention of the fuel filter in the maintenance guide - just visual inspections of the lines and the fuel cap gasket every 30K miles.