Yeah, what he said ^^^
It may be kind of ghetto but for my 14' boat I just get a gray 10'x20' tarp every year that covers the boat and lashes down with bungee cords on the corners and 2' camstraps in the middle. Its $20 at the Great Satan of Retail. Put steel soup cans on the oarlocks to protect the tarp or they'll poke right through it. When I go boating, the tarp gets folded and tossed it into the back of the car to either use as a rain tarp in camp or to cover the boat if I have to leave it parked in a public place overnight. Another good thing about a tarp is the "out of sight, out of mind" factor - a whitewater raft attracts a lot of attention and usually has lots of shiny, expensive looking things just sitting out for the taking. Living on a corner lot, I've noticed that when I've got the boat uncovered almost every driver that passes by gives it a glance, with the boat covered it just blends in with the shrubbery.
The tarp gets replaced yearly at the start of the season - it gets beat up enough over the year to be rotated to camp kitchen floor tarp and then goes into lawn & garden use.
I can't imagine hitting the highway with a fabric cover on a boat - it seems like the wind would just beat the hell out of it during the drive. Getting road muck on the boat isn't much of a concern as I usually take it to the boatwash when I'm on the river anyway.
Here's what it looks like (you can decide if its worth the extra $300 for the custom cover):