I think that the carbon fiber would be nice but much more expensive than the fiberglass. Although the weight diference I think would not be that tremendous, well not enough to justify the extra cost anyway. Your probably only looking at maybe 20-25 lbs lighter than the fiberglass. I have been looking at the Versacover tonneau lately (I think it and undercover are the same) made of ABS polymer and weigh only 50 lbs or so and this I do believe would be much lighter than even the carbon fiber. The only downside I can think of is that they have a slight texture to them which would make them look a little funny if you painted it unless there would be someway to smooth out that texture.
In case you want to check out the cover here is the link.