If everyone watched both episodes the Mythbusters did on MPG myths, you would know they also tested a
tonneau cover, on the same truck, in a "he-hash" episode.
Results...
Tail gate up was the base line
Tail gate down netted a loss
Gate net netted a loss
Canopy netted a loss
tonneau cover netted a gain
Look it up, there are sites that go into more detail about the episode.
Now, all that said...I have seen an improvement after installing my
tonneau cover, but I also slowed down from driving 65- 70 mph, to driving 55 mph on the freeway no matter what. 55 mph is what's giving me my biggest gain, 2-3 mpg saved. I am sure the Tonneau helps, but most of it was attributed to slowing my ash down.