As noted, because the actual brakes are not used all that often or intensely, they will often end up with a coating of rust on their surface. When driving somewhere where there's no traffic and you can safely do this, try getting up to say 100km/h and doing a panic stop. The ABS should prevent the tires from skidding and flat spotting. Do a couple of those, and you should polish off your brake disks.
Surface rust isn't a big deal except for making the brakes noisy...but, an occasional panic stop when safe should polish them off to solve that issue, at least for awhile. Generally, after a rainstorm, the first couple of stops are a bit noisy, but after that, they quiet down for me. My driveway is fairly steep, and when leaving with a full battery, regen is inhibited and you're actually using the brakes versus regen initially...I definitely notice the difference between regen slowing the car and the actual brakes!