RTF is correct. River Horse was trailered a few times to get around obstacles like dams and over the Continental Divide. While Moon's objective was to cross the nation by water, the purpose of the trip was more to observe and learn things about the nation as he went rather than travel every inch of the way on the boat's bottom.
In this respect it was very much in the style of his previous book, Blue Highway, in which he traveled the country by road.
And obviously a 22 foot C-Dory is a far cry from a 30,000 pound diesel cruiser. Getting one of them across the country will either involve a professional trucking company or the Panama Canal.