Bed rail caps

You've piqued my curiosity... why do you want to cap the holes?

To keep them from filling up with dirt and Debre. I don't see any use for them except maybe installing stake rails.

Does anybody use these holes? If so what for?

I use them for my chain saw scabbard and a Moose saddle box. There are tons of accessories you can get that use these holes. If you just want to plug them, there are a few posts on here where guys have made tie downs that are similar and less costly than the Polaris branded ones. At least then they would be plugged but would have a function. That would be a ton of tie down points!