Treasure Island begins with the arrival of the mysterious "Captain" at the Admiral Benbow Inn, singing about "fifteen men on the dead man's chest." The first question he puts to Jim's father is whether the inn gets "much company." He seems to be only making conversation since the question follows his observations that the inn is situated in a "handy cove" and provides a "pleasant sittyated grog-shop."
Evidently, the sly captain was leading Jim's father to provide an answer that would have made him, the captain, take his leave. When Jim's father replies that the inn isn't at all busy, although he wishes it was, and the captain replies that it's exactly what he's looking for and announces his intention to stay for a while.
It soon becomes apparent that the man, who they later learn is Billy Bones, is there to hide from someone, in particular, a "seafaring man with one leg." He pays Jim to keep a lookout for the unwanted visitor and to warn him if he should ever see a man like that approaching. Therefore, the reason he chooses to stay at Jim's family's inn is that it is isolated and provides him the best hope of avoiding his old shipmates.