Assuming that light reflections from a shiny rod surface or from the finish on the windings can spook fish, I conclude that matte finish is the best way to play it since fly fishing involves more close quarter fishing. You may never need it; but if you need it, you have it.
But not all blanks are matte finished. Is there a safe way to dull the finish on a shiny blank?
And, of course, what is a good product to use to put a matte finish on the rod windings?
I usually take some extra fine steel wool (0000 grit) to a new rod to take off the shine. I have definatly seen a rod flash spook fish.
If you want a less aggressive abrasive look at some of the auto body painting abrasive/pilishing compounds. They come in a series of grits and are used to remove swirls from painted surfaces. Depending on the grit size you can use them to polish to a brite fiish or matte finish.
kengore,
There are a lot of gawkers and not many talkers. You are the only one out of over 100 viewers that replied 
Thanks for confirming my suspicion about the flash. Actually I was “fishing” for a better way to do this. On inexpensive graphite rods I have created a stealth finish. I worked my way up to something that worked by trying common abraisives.
These didn’t work:
Soft Scrub
Comet
Turtle Wax Rubbing Compound
Scothc Brite No Scratch Pad
Since it was a cheap rod, I also tried etching it with lacquer thinner and mineral spirits. Hats off to Rhino, that didn’t work either.
This finally worked: 
Scotch Brite Heavy Duty Pad
There’s just enough grit to dull the finish without aggressive scoring. The pad provided a good way to apply pressure evenly. Wetting the pad controls the dust nicely.
Some day I will give steal wool a try.
PS I was glad to see that the Cortland Rod I just bought came with a matte finish blank though the wrappings are shiny epoxy. Oh, well. 
Bear,
You might want to try using some Lapping Compound on a cheap piece of graphite to see what happens. I used to use it to polish the inside of rifle barrels.
God Bless,
Hey Kengore,
The easiest way that I know of to make a glossy blank matte is to use a grey (very fine) 3M scotchbrite pad. If you carefully rub the blank with one of these pads, you can remove the gloss and not harm the actual graphite fibers. I have also used the finest steel wool that you can find (OOOO in my case) and that also worked very well.
All it takes is a bit of patience and some elbow grease and you can get a very nice looking matte blank.
HTH,
Lou