It seems only available behind a pay wall, but the National Research Council of Canada did wind tunnel testing of pick up tailgates. The short form of that is to keep in up for most trucks.
They also looked at a partial tonneau cover. Why partial? Because GM had a patent on the use of a partial one because helps with aerodynamics. I had one on the Ranger because of this paper. Can't say how much it helped at this point since the data is gone, and I no longer have the truck.
So tonneau cover will improve aerodynamics. Depending on the commute, that might not equate to improved fuel economy. Even then, the efficiency gains likely won't cover the cost of the cover. If you want to cover the bed for other reasons, it can be a bonus.
Article on the paper:
http://www.nrc-cnrc.gc.ca/eng/achiev...down_myth.html
The paper source:
http://search-recherche.nrc-cnrc.gc....ofile=_default