I'm not sure what you mean by "cylinders"... the brake master cylinder is in the engine compartment and isn't an area that would rust. The calipers could be a bit rusty on the outside but that is definitely not a problem. It happens to pretty much every car over time. It is unlikely that the pistons inside the calipers would become rusty, and that's also not something you could observe without at least taking the caliper off and removing the brake pad. Based on this, I'm assuming that the rust you see is actually on the disc, or rotor. Generally speaking, a bit of surface rust isn't a problem on rotors. The rotors on pretty much any car will get a little surface rust if the car is left parked and there is a rain storm that gets them wet. Normally the pads will just "wipe" this rust off with the first application of the brakes and there's no real harm done anywhere. There may be some "grating" or "grinding" sound the first time or two you apply the brakes as that rust gets cleared off, but the sound should subside after that.
If you are getting grinding sounds from your brakes more than just the first few times you apply them, you may need to have the rotors turned, and may need new brake pads, as well. I doubt that Toyota would cover this because oxidation of the metal brake rotors doesn't indicate a material or manufacturing defect. With that said, Toyota might turn the rotors for you at no cost as a courtesy, but I wouldn't bank on that.
I suggest you go take the vehicle for a spin, do some relatively hard braking while you have it out there, maybe some braking in reverse, too (that may be the best way, actually, because I believe the regeneration system doesn't come into play when in reverse), and then see if the rust is gone.
DO NOT TOUCH THE ROTORS AFTER DRIVING - they could be very hot.
Good luck!