How do I keep nails from pulling up on my hardwood floors?
If I understand correctly, you have small-head nails driven through the flooring planks vertically and flush with the surface. They're working upward from the up-down flex of the boards as you walk. 

I would acquire a nail set the correct size for your nails and drive them slightly below the surface of the flooring. This will serve to lock the nails into the finished floor, and any movement will occur in the subfloor instead. You could then use a colored nail hole putty to hide them.

Another solution would be to pull the nails with a needle-nose plier or other similar tool and replace them with slightly longer, larger, or ring-shank nails to give them a stronger grab.