http://www.bassmaster.com/blog/bass-boat-cover

Here is an article on this very topic. Zell Rowland actually disputes the claim that a cover will reduce your fuel mileage and a proper fitting cover will actually increase your mileage becuase the air will flow over the cover and not into the boat, which is where the drag is created.

"...Rowland says boaters would be surprised by the amount of road scum that will collect in the carpet or upholstery."