No matter if you have a graphite, fiberglass, or a bamboo fly rod after use they get dirty. Along with the dirt & grime that rods acquire from use, they sometimes get watermarks on the shaft from being in contact with a wet fly line. For these problems that arise from normal use (we're not talking about damage here), it's a good idea to gently clean the shafts of the rod with some liquid window cleaner (like windex, etc) & a soft, clean towel. Spray the window cleaner onto the towel & wipe down the rod shafts gently. Then follow that by wiping the shafts dry with another soft, clean, & dry towel. Make sure to get the area beneath the line guides & the guides themselves.
Next, if you have a bamboo rod with varnish, or a fiberglass or graphite rod with a gloss, shiny finish, go over the rod with a good furniture polish - the same kind you use around the house (Old English, Pledge, etc). Again, spray the wax on a clean, soft towel, & wipe off the wax with another dry towel. Make sure that you get the line guides as well but make sure you get all the excess wax off the line guides. If you don't, it will build up on the guides & slow your fly line down.
DO NOT WAX THE FERRULES!!! This is especially true for the metal ferrules of a bamboo rod. Never ever wax the ferrules. If you need to clean the metal ferrules of a bamboo or older fiberglass rod, put some rubbing alcohol onto a clean, soft towel & wipe the ferrules with the alcohol. Then wipe them again with a clean, dry towel. Make sure the towels are clean & do not have anything on them that will scratch the ferrules. To clean the inside of a metal female ferrule, dip a cotton swab into some rubbing alcohol & swirl it around inside the ferrule. Keep doing this with a fresh cotton swab each time until they no longer have dirt on them. Then dry the inside of the female ferrule with a dry cotton swab before assembling the rod.
If you have a rod with a matte finish, just clean the rod with the liquid glass cleaner, or warm water only. Don't wax the shafts of the rod, but you can wax the line guides & the guide wraps if you wish.
Finally, after you've cleaned & polished the rod, I like to go over it one more time with a "dry sweeping cloth" (like "swifter") that are available at most retail stores. This really polishes the rod up & gives it a nice appearance. It also removes fingerprints & other smudges.
Regular cleaning helps to protect the finish of the rod & to protect the guide wraps & labels or inscriptions on the rod shafts. If you take the time to clean your fly rod & keep it looking good, you'll be going a long way to getting more years of use from it.