It is related to the idea of the land of Faerie I think in "Smith of Wootton Major".
And sort of like why we don't kill all the tigers and lions and wolves in our world.
Who says it would be a beautiful country if he killed all these creatures? And what would that make him into?
He might have been able to make it into a "tame" world like the hobbit country. A world with no adventure, no challenges. For a short while. But that's not where he was at. There were plenty of humans to do that, and they already had been through that part of the world mastering it and destroying things and making weapons etc. That's their way but not Tom Bombadil's way.
And - you can't actually make the world into a perfect place.
Remember for instance Gandalf saying to Gimli: "Yes, I am dangerous, you are surrounded by dangers Gimli, you are not likely to see anyone more powerful than me unless you meet the Dark Lord face to face."
They are only evil to the hobbits because the hobbits are straying out of their normal habits and paths and behaving in a very unhobbit like fashion - and the creatures themselves also, stirred up by the ring doubtless, are behaving uncharacteristically also, such as old man willow waking up when he should be asleep.
It's sort of like saying that you should kill all sharks because some of them have occasionally killed human swimmers.
They are part of the pattern and energy of the place. And it's not Tom Bombadil's role to battle with those energies, that's just not how he works. He just sings to them. And they recognize him and his mastery because he is true to himself.