Well... I've read it now, and admittedly the author makes a good case for his theory... but I'm still not entirely convinced. Some things he writes really seems like grasping at straws to me; for instance, Goldberry's green garment indicating that she is Yavanna because Yavanna also wears green, or his dismissal of the whole 'daughter of the River' thing because of the other things 'unrevealed or unexplained', such as Gandalf and the Eagles not being revealed as Maiar, the 'origin of the orcs' thing and even the rumour of Rohan's selling horses to Mordor.
Also, he rules out the possibility of Tom being a Maia because 'there is no Maia in the Silmarillion who matches Tom's general character'. Seeing as how there were supposedly hundreds of Maiar, I think the author is a bit over-eager to skip right ahead to the Valar.

On the other hand, maybe I'm simply sticking my head in the sand because the idea of two Valar taking up a life as Tom merry dol Bombadil and his spouse is just not what I want my Valar to do. I liked the simple 'enigma' solution better.

One last note: if Aulë and Yavanna became Tom and Goldberry, they must've done so immediately after the War of Wrath, as I think Elrond tells the Council that Tom was already around when he was young. I think that this would kind of rule out Aulë's supposed interest in hobbits being the reason for assuming the Bombadil persona, as hobbits aren't even mentioned until a good way into the Third Age, and Tom did apparently show himself to the Elves in this form (or at least that's what I make of Elrond's remark, without having the book to hand).

You know, I came from a Tolkien messageboard (which I haven't visited in a long long time now), where I never took part in the book discussions, and now, on a Total War forum, I'm finding myself discussing the nature of Tom Bombadil, one of the things, along with Balrog wings and the origin of orcs, that one should avoid discussing. Kind of ironic, if you ask me.