The Archangel Michael in Middle-earth

[Aaron]

An interesting idea, but I think it's a faulty comparison.

Considering Tolkien's own deep Christian value system, were Tom meant to be analogous to Michael, there would not be so much about his portrayal which was so open to interpretation. I have spoken before about the duplicitous nature of Tom Bombadil, and about how I believe he was Tolkien's commentary on the duality of nature being both a source of great beauty and also mystery and danger.

Were Tolkien attempting to use Tom as a surrogate for a figure in Catholicism, I simply don't feel the depiction would be so hazy and open to interpretation.
It's true, of course, that he has many characters who are morally complex - but the religious authorities of his world are not so. They are good and do good, and those who err are definitively punished.
Bombadil doesn't really fit that category.