The author of this has clearly not read much of Tolkien's legendarium beoynd the LoTR... This is a whole lot of speculation that does not at all fit into Eä, the World that is. Though indeed one might say the same of Bombadil, it is far from clear what role he has to play in Arda, and Tolkien took his cosmology very seriously, so there is every reason to think this mystery of
who the hell is Tom Bombadil? is intentional. But the reasonings of this article is exactly those of conspiracy theorists, not those of any serious Tolkien scholar. Seemingly relying on “No hobbit has ever heard of him,” “Elrond, the greatest lore-master of the Third Age, has never heard of Tom Bombadil” as implicitly implying “therefore there must be some great dark secret,” Gandalf's explanations he simply dismisses as not “the true one.” Tolkien was a philologist, familiar with and directly inspired by many different mythologies, for example Väinämöinen, a hero and demigod of songs and poetry from finnish folklore has been pointed out as a possible inspiration for Bombadil. Though from his close connection to nature one would rather expect him to be a sort of demiurge than a hero, neither evil nor good, and indeed as opposed to Väinämöinen whose adventuring is due to his seeking a wife, Tom
has a wife and makes a big point out of this, he is content, and has no desire for evil. If I may continue my rant I'll add that the very creation of Arda is by music, taught by Eru Ilúvatar, the One, to the Ainur. There is little doubt that Bombadil is among the Ainur, one of the Maia on par with Gandalf and Sauron. It seems entirely plausible to me, that Bombadil indeed is as he says, the oldest, of special significance to Ilúvatar, prior to Arda and whatever may be happening in it.
I'll also add that I have never heard of any Tolkien enthusiast not liking Bombadil before this. I suspect the author of this article is among the minority who thinks that abruptly breaking into song is lame, mistakenly of course, hehe.