303 will wash off with the first site of water. Any decent Vinyl/Rubber (exterior) protectant will work well. I recently used Finish Kare Top Kote dressing on mine, and it still looks like new -- after 2 rainfalls. Truxedo makes Pro-TeX protectant for tonneau covers. You can often find it at a truck accessory store (Line-X, etc.).
That's weird I've never had that problem and the product is literally designed for use on boats. In fact, there are plenty of "how to" videos on using 303 for marine applications.