There are many invasive species besides zebras and quaggas. New Zealand Mud Snails (which are in parts of Wyoming and much of the West) and many invasive aquatic plants can be spread by boats.

I don't have a problem with this kind of fee (granted I do not own a boat) and, if nothing else, the fees help raise awareness of the threat presented by invasive species. The revenue generated from these fees can go to prevent the spread of invaders, as well as to attempt to rehabilitate areas that have already been invaded (no easy task). Considering all the other money I pay for fishing gear and gas to get to the river, I am willing to pay a few extra bucks a year to ensure I have healthy rivers and lakes in which to fish.