Out of the 4 player encounter cards in the game, Tom Bombadil has to be my least favorite.
First off, there's the consistency issue; unlike the other Encounter cards, you can only ever have 1 copy of Tom Bombadil in the encounter deck at a time. This makes him even more unreliable than the other Encounter cards, which are already pretty inconsistent, and 2 resources for something that might work is typically not a good deal (c.f. Needful to Know). Honestly, something that I think would make the Encounter Cards much more viable is a simple addition to the rules of player cards with Encounter in the form of, "Cards with the Encounter keyword gain "Shadow: Shuffle this card back into the encounter deck." Of course, that would also either break or necessitate an errata for Wind from the Sea.
Said Wind from the Sea also illustrates the main problem with Tom Bombadil: their shared lack of surge. Ranger of the North and Eagle of the North are strong, especially the latter one, but they don't completely break the quest phase when they're revealed; a beneficial card was revealed from the encounter deck, yes, but you still have to deal with a regular reveal as well. This decreases the random chance associated with them by making it less impactful whether they're revealed or not. If they aren't you have to deal with a regular encounter card, but if they are you still have to deal with that encounter card. Tom Bombadil and Wind from the Sea, on the other hand, don't have surge, meaning that you either spent 2 resources to water down the encounter deck slightly if they're discarded in some form or made it so that, barring quest effects, one player just doesn't reveal encounter cards during staging. This is really bad game design, making it so that the player's success is more dependent on whether a specific card gets drawn from the encounter deck than whether they manage to play well.
Wind from the Sea and Tom Bombadil's shared "Remove them from the game" makes this even worse, adding even more variance to already random cards. If Wind from the Sea or Tom Bombadil either doesn't get revealed at all or gets revealed on a turn where you can't really do much with them you effectively wasted 2 resources, whereas if they are revealed at a time that you can make use of them they can all-but win you the game. This kind of random chance, where you either straight-up win or waste a card and 2 resources, is more reminiscent of the Mirkwood cycle or even the Pokemon TCG than the developed game we know and semi-love.
Until Tom Bombadil gets erratad to gain surge, if you want a game more based on skill and strategy than a random card draw, you'll find it wise to act like Peter Jackson did and simply cut Tom Bombadil.