I agree with all of the other posters. While one does not have proof, I would like to think that Huck was a character that Twain loved very much. With as important as a character as Huck has become in literary history, it be a shame to find out that Twain despised him.
Mark Twain liked Huck very much - possibly even to the point of envying some aspects of Huck's life. Once he ran away from his pa, Huck had the freedom of the river, to go wherever the water took him and to move on to the next place whenever he decided to go. Mark Twain spent enough of his time exploring the world to make me think he may have wished he could join Huck and travel with him!
Twain must have loved Huck since he followed up The Adventures of Tom Sawyer with a book of Huck's own. Huck is a far more complex character than Tom (as is The Adventures of Huckleberry Finn), and Twain seems to delight in placing Huck in all sorts of predicaments before finding him a way out. The friendship and loyalty that Twain establishes between the two boys is a strong one, and it carries over beautifully in Huck Finn.
I think the fact that Huck's book is more complex and sophisticated than Tom's demonstrates that Twain related to him more. Tom's book is about childish hooligan games, but Huck's is about moral questions.
I think he likes Huck. I think he is using Huck to explore his attitudes towards the rules of society. I think he does not really completely approve of those rules and so he sees Huck sympathetically. We can see that he likes Huck because he allows really good things to happen to him. By the end of the book, Huck is like a second protagonist.