Well, there are different methods of cylinder honing, and the one that most folks are talking about in this thread is flex-honing, the type that is typically performed by hand with a portable drill motor. This leaves a cross hatch pattern on the cylinder walls, which serves two purposes. One, to help new rings 'wear-in' with the cylinders, and two, to cause a small amount of oil to cling to the cylinders, which helps with lubrication and sealing to maintain a higher compression for a longer service life.
I would be concerned that after only 3000 miles that none of the previous cross hatch remains, as it is quite common for some amount of cross hatch to still be visible after ten times that mileage. Is it possible that the flex-hone was too small (they require some compression to work effectively) or that it was used too quickly or lightly when this operation was performed? Although you're not experiencing (or noticing) any compression or oil useage issues at this time, the cylinders may in fact be wearing faster than they should given the absence of any cross hatch after such a short time.
If you checked or sized the piston ring gaps when the engine was assembled (3000 miles ago), check them again now and compare, as it is possible that the rings are wearing too quickly and causing the cylinders to wear too quickly as well. If the gaps are the same (or only differ by a thousandths or two) then the cross hatch was likely only very light and should probably be re-done. If the gaps have grown, then I would replace the rings and perform a fresh flex-hone before reassembling the engine. Also make sure the top ring wasn't inadvertently installed upside down, as this can also be the cause of accelerated wear on the cylinder walls.