Sure, I can understand on a microscopic level you're going to reintroduce carbon, but it's still SIGNIFICANTLY cleaner and definately faster than using a rod and patch. Rather, with a rod and patch you leave more carbon in there unless you use a ton of patches, which is your choice of course.
I don't get too attached to the patches... I easily go through two dozen patches... same for Q-tips... honestly considering buying stock in them.