From the outside, it looks like Milo ends the book basically where he started: in his room. The tollbooth's gone, so there's no evidence of the magical journey he just took, and it turns out he's only been gone for a couple of hours. It's as if his venture to the Lands Beyond never took place.
It's really too bad. All those exciting adventures, the things Milo learned, the people and characters he met – and from the outside, it's like Milo just spent the past few hours in his room, doing nothing.
Depending on how realistic your view of the book is, you could say that maybe he didn't go anywhere, maybe he was in his room the whole time. But you know what? It doesn't really matter. Milo clearly did go on some kind of journey: whether it was real or imaged is kind of beside the point (at least in the discussion of the ending!).
On the inside, Milo is totally different. During his time in the Lands Beyond, he acquired a whole new set of values and interests. At the beginning of the book, he was super-bored by everything: "When he was in school he longed to be out, and when he was out he longed to be in. On the way he thought about coming home, and coming home he thought about going. Wherever he was he wished he were somewhere else, and when he got there he wondered why he'd bothered. Nothing really interested him – least of all the things that should have" (1.2). The Phantom Tollbooth's first paragraphs show a boy who has a lot and is pleased with nothing.
In contrast, at the end of the book, Milo is excited by everything around him, and inside him. He's excited by the contents and skills of his own mind, and what he can do with that mind. In the Lands Beyond, he thought that his quest was rescuing Rhyme and Reason, and restoring rational thinking to the Kingdom of Wisdom. But don't you think his quest is about way more than that? In a way, he's actually rescuing his own imagination for himself. The book's very last lines have Milo saying, "Well, I would like to make another trip […] but I really don't know when I'll have the time. There's just so much to do right here" (20.19).
Milo loses the tollbooth, so he can't go back to the Lands Beyond again, or meet up with the friends he left there. But now, he doesn't need some outside object to have adventures or enjoy himself. He's figured out how to enjoy the present, to soak up his surroundings, and to make magic where none seems to exist. He's gotten out of the Doldrums, for good.