They are common points of contact from road debris, as well as places that tend to rust out first on a vehicle. What they are probably trying to do is protect those surfaces. However, this can be a double-edged sword - what is meant to protect can also act as a trap for dirt and moisture, thus causing rust. If they are sealed enough to keep those things out, along with good corrosion protection on the metal, they might work. This is going to be largely dependent on the manufacturer. 

As for what is under this bodywork, it should just be painted metal, like the rest of the car. Usually this trim is held on with a double-sided adhesive tape. So it's possible that it could be removed if you hated it.