If you are not seeing metal then you can just use touch up paint. I suggest going to your local Toyota dealer for the touch up paint so it is factory match. Just know that you will notice the touch up in the finish because it will be hard to get the surfaces to match up again. A body shop would sand down the area, prime, sand, spray, then clear coat, and buff to smooth/blend it all out.
Either way, put some paint on those chips on the metal parts. Paint primer is porous so it is susceptible to water getting though and hence, rust.