Billy Bones—also known as the Captain—is hardly a model guest. While he is staying at the Admiral Benbow Inn, he is constantly abusing his hosts as well as frightening other guests. Billy Bones is constantly cursing, singing tawdry sea chanties, telling terrifying stories, and drinking himself into belligerent oblivion. He even gets into a sword fight with Black Dog right there at the inn. While it is always good for business to have a guest stay long term at an inn, Jim's father would much rather rent the room to a better-behaved guest. It even seems that the Captain has fallen behind in paying his bills to the inn, so they have not even received fair payment for having to play host to the old pirate.
We also learn at the beginning of the story that Jim's father is in poor health. We can only imagine that dealing with the likes of Billy Bones while gravely ill makes it even that more insufferable. Jim's father may also be worried about the influence that The Captain has on his son. While Jim is in many ways terrified of the pirate, he is also very much fascinated by him. Despite the danger, there is a certain allure to Billy Bones's pirate tales. It is possible, knowing that he is likely going to die soon, that Jim's father worries he won't be around long enough to steer young Jim away from a swashbuckling life at sea.