Bombadil was one of the most important pieces of world building in LOTR, and that's not a joke. He's clearly a being of great power. He holds absolute sovereignty over his domain, such that even the trees and the undead bend to his will. And there is absolutely no cogent information or backstory on him, whatsoever. At all. Bombadil is printed proof that Middle Earth has a lot more going on than is touched on in the story. If Bombadil is an unexplained Great Being then it stands to reason that there would be more, beyond Sauron and Sauruman and the characters we meet directly. Bombadil is a signpost pointing off-screen and saying "Hey, there's more stuff over this way".

He may be crazy, and silly, and poorly explained, but that's all for a reason. Tom represents the "etc." at the end of the list of beings in Middle Earth. He is an open end implying the existence of more like him.