They say no on the tonneau. Here's some info:
PickupTrucks.com Forums: Gas Savings With Tonneau Cover?
Another test says yes:
Testing The Tonneau/ Fuel Economy Theory - Ford Truck World Articles
The mesh probably breaks up the wind back there and helps direct it out the bed.
Conclusion? I bed cap that slopes from the top of the cab, down to the tailgate would be ideal. Jury's out for the tonneau - needs some real-life testing. NasTrucks have them. I have an aluminum tailgate with louvers for towing my 5th wheel, but I can't tell the difference in FE.