I am not sure where I read this, but it seems to me that Tolkien confesses to not liking Sam much and distinctly disliking the Gaffer because of a certain dumb arrogance. It's probably in the letters, the one book I would like to have and don't. Somewhere else, Carpenter's bio probably, it says that he hated the army but was very impressed with the moral fibre of the common british soldier and someone (Shippey?) feels that Sam comes from that experience.
I haven't liked Sam much either. He's irritating and kind of ignorant. However, that's not the point, I think. Not for us nor for Tolkien. I know people I love to be with whom I don't much respect and I know people who are, for me, a bore, but are far far better human beings than I. We can't rate people because of their entertainment value. Sam is a great hero whether or not he is the ideal dinner guest.
For that matter, these books are great books because they are more than just entertainment. They are even great entertainment because they are more than entertainment.