I have been using this matte paint protector from a company in Quebec on my matte finish carbon bikes. It's almost invisible once applied. The matte clear isn't even listed on their site, but email them and you can order it. I paid $30 for a 2 foot x 5 foot piece, which is plenty for 2 bikes.
http://vvividvinyl.com/
The bike in this article is covered in the stuff; top tube, down tube, seat stays and chain stays. You can see a seam across "Norco" in one of the close up photos, and you can barely see a difference in the covered vs. uncovered side.
http://nsmb.com/cane-creek-double-barrel-coil-climb-switch/
I ordered the same stuff from those guys. I think I ordered it from their ebay store as they had the matte on there.
Pretty good product but, as all wraps, takes a bit of effort to get on good. I used a heat gun on low and waved over areas with bubbles to take care of that. The matte definitely is matte and doesn't look much different than the matte paint.