[MattConfluence]

It's a fun read in a fan-fiction sense, but when you look at the out-of-universe story of the events of Tolkien's life and his writing process it becomes clear that Tom is not meant to be any kind of evil.

Tolkien wrote a silly whimsical poem about one of his children's toys that they had named Tom Bombadil. In this tale he lives in a dangerous environment, but he is able to overcome the dangers and get his happy ending.

When Tolkien later was writing LotR, he drew upon his former work and put in the silly whimsical Tom as an early encounter for the Hobbits just as they are leaving the Shire and starting their adventure. This story arc delivers some early exposition about the world in his dialogue, it shows that the Hobbits are hopelessly unprepared to stand up against any foe such as Old Man Willow or the Barrow-Wight and need rescue (this way they can have character growth and become Heroes by the time they return to the Shire) and it gets the Hobbits armed for their quest towards Rivendell (and most importantly to put the right kind of blade into Pippin's hands for later).

In a more thematic sense he is just part of nature, not evil but also not actively looking to do good, just existing. He is master of his domain in the same sense a big moose might be the "master" of his local forest, he's the biggest around and isn't threatened by anything else, but he has no human desire for expansion and doesn't push back when civilization comes around to turn the land nearby into farmland either, just keeps to himself. He doesn't try to tame the angry trees because it's just protecting it's territory, as is natural, nor does he try to "exorcise" the barrows because nature doesn't actively go about trying to undo the evils created by man.

[joe_the_user]

The thing about Tolkien (and I think good story telling in general), is he gives a feeling of consistency, depth and complex choices. But that's completely different from needing fine-grained consistency between chapters of a long book. I'm not a Tolkien expert but I think are a whole variety of "plot holes" one can point to but these don't particularly matter for the development of the story, where the main thing is the suffering and redemption of the main characters which only has to feel real and as well as feeling dramatic.

I think Elrond hadn't heard of Tom just because that made the council scene more dramatic, for instance.

[rottingchris]

Elrond had heard of Tom Bombadil.

    There was silence. At last Elrond spoke again. [...] The Barrow-wights we know by many names; and of the Old Forest many tales have been told: all that now remains is but an outlier of its northern march. Time was when a squirrel could go from tree to tree from what is now the Shire to Dunland west of Isengard. In those lands I journeyed once, and many things wild and strange I knew. But I had forgotten Bombadil, if indeed this is still the same that walked the woods and hills long ago, and even then was older than the old. That was not then his name. Iarwain Ben-adar we called him, oldest and fatherless. But many another name he has since been given by other folk: Forn by the Dwarves, Orald by Northern Men, and other names beside. He is a strange creature, but maybe I should have summoned him to our Council.'

[TheRealPomax]

It's interesting that this description is apparently "evil", even if in this framing Tom predates all, and everyone lives on his unceded land. You'd become "particular" about your role after living through several ages of that, too.

Rather than evil, it's more "biding their time until that injustice can finally be rectified". In this post's framing, literally every humanoid race is by definition an (unwitting) invader.