My logic is this:
If i'm done shooting for the day, i will use the cable for faster transfers if i have a lot of images and or movies (especially) on card.
If I'm going back out shortly and don't have time to charge my battery, i'll use a card reader. I also use a card reader when I have less images.
As far as what Nikon was thinking? I'll bet it boils down to business. Just like Apple does, ya? It's common practice these days. Android phones sometimes have weird sized micro-usb connectors and it's hard to find a cable to charge them with sometimes.