The paint shop at the assembly plant needs large holes for the doors to drain. At the same time, the holes want to be small in order to reduce the amount of road noise, wind noise, air leakage in the cabin. So Ford's solution is to install these black clips after the car is painted.
I remove these from my cars. Leaving them in impedes water drainage from the door, which causes rust on that bottom edge. For me, they are not worth the 0.1% (or whatever) NVH improvement (doesn't everybody just turn on the radio anyways?)
Plus, now I have some nice large access holes to spray in some WD40 into the door periodically, as an additional anti-corrosion measure.