I used the boat a lot at the start as well, it's just that once you get improved swimming on your horse and more stamina it just feels easier to use your horse to go in an (almost) straight line to your destination rather than having to follow all the meanders in the river. It's not that I dislike using the boat, far from it, it's just that a fully upgraded horse is more practical with getting around.
Also, it's not just clipping the shore but also if some dumb bastard decides to row their boat in front of yours and you smash into it it also cancels the auto sailing feature.