My first reaction was that Boone died at the Alamo and then after further reflection I remembered that it was Davy Crockett that died at the Alamo.  As to why Boone is only remembered in Folklore, that is a good one.  I would tend to say that because he was a legend in his own time that the stories and remembrances have only grown with time to the point that the real person is lost in the fog of anecdotes and apocryphal stories.

In a lot of ways it's amazing that Boone is remembered at all.  In spite of his reputation he never really accomplished anything of significance: he didn't discover Kentucky, didn't settle it first, underwent a court martial for treason, had Tory connections, etc, etc.  To be sure, he lived a fascinating life but there were many other pioneers, many he knew, who did more than he ever did that have been forgotten.  The reason Boone is remembered isn't necessarily because of what he did, but because he was the focus of John Filson's narrative – in short, he had a good press agent.