I've always used keyboard covers on my Macs because the shiny black keys drive me crazy. Never had a problem with them. After over three years now my 15" rMBP keyboard looks brand new.
I predominantly use Moshi keyboards and they have one for the Retina MacBook. It's super thin and even has this little sticky strip between two rows of keys so it stays on. No problems so far.
If you do use a keyboard cover, you might find it making faint dust marks on your screen. These easily come off if you clean them with a micro fiber cloth or something similar. I've had no lasting problems with this. For example, my rMBP screen is fine. If I'm going to keep it closed for a while (like using in clamshell mode) I'll take the keyboard cover off.