Do you have any idea about the provenance of this character? He has always seemed a little out of place to me. Like a children's fairy tale figure who somehow got stuck ina much more serious book.
Perhaps Bombadil has a different relationship to Eru Ilúvatar, and to Arda than do the Valar or the Maiar. In some ways, Tom's relationship to Arda is clearly deeper than that of the Valar. In fact, I would say that the Valar are primarily concerned with Arda as the realm of the Children of Ilúvatar, while Bombadil is more concerned with the life of Arda itself, and especially his own special region of it.The Children of Ilúvatar would be another example of such separate relationships to Arda and Ilúvatar.
@Alex - There is a vast amount of good stuff on the web about Tom Bombadil- I couldn't begin to summarize it. But we have to find something which makes sense for us. Joel makes an excellent point - Bombadil comes across as a one-off character, not a member of a larger group. Explaining him as a nature spirit seems to miss his very specific, human, down to earth quality - explaining him as a Maia (minor deity, or angel, like Sauron, Saruman and Gandalf) seems to neglect how very different a kind he seems from them. For me, the key fact is that Tolkien makes what superficially looks like a clear, repeated contradiction that both Bombadil and then Treebeard are the oldest living sentient creature. I think this is resolved by Bombadil being the oldest, but one of a kind; and Treebeard the oldest of the free peoples (Ents, Elves, Dwarves and Men/ Hobbits) - so Bombadil 'does not count' in this scheme. Other 'one off' creatures perhaps include Ungoliant - the giant spider ancestor of Shelob - who seems not to have been made by premier god Morgoth, and had power over him/ he had no power over her; and the watcher in the water outside Moria.
Remember that when we are in Tom's world, trees and rivers have spirits and personalities, etc. That is not the world that we move in elsewhere in the story.And the fact that Tolkien is big enough to encompass such contradictory -- but ultimately complementary -- worlds adds to the reality of the whole, rather than detracting.
@Joel - One of the fascinating things about Tom is that he does not try to eliminate the evil from his land. He rescues the hobbits from Old Man Willow - but leaves him alone after that. He tolerated the Barrow Wight for hundreds of years before chasing him away and breaking open the barrow to rescue the hobbits. He seems to accept things as they are, does not try to shape them, and does the bare minimum to protect the innocent in the short term. Very much a hunter gatherer, animistic way of living in the world.
Tom seems to have been edited out of the movies entirely. I need to reread the books. He seems to be a part of a homey folk-magic world, a potentially dangerous but more innocent world than that envisioned elsewhere in the trilogy.
There's also Caradhras, the Redhorn mountain, who appears to prevent the passage of the Fellowship over his pass through a deliberate manipulation of the weather. Aragorn (or was it Gandalf?) suggests that Caradhras is older and independent of Sauron. What was never explained was why Caradhras, supposedly not being under Sauron's control, should care to prevent the passage of the Fellowship, unless he were in league with Sauron himself for unknown reasons. I wonder what kind of promises Sauron could make to such a being - maybe not to allow any Orcs to gouge him out with tunnels?