These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The book's mythical style is probably what makes it work. Old stories are riddled with Larger Than Life figures that cultures associate themselves with. Lúthien comes as this, and it is pretty clear the stories are painting her as some sort of great example of how to behave.
Complete Monster: Melkor, later known as Morgoth Bauglir. Melkor begins life as one of the Valar, but his spite and arrogance precipitates his steady downfall into evil. Melkor begins by destroying the great lamps of Valinor, and by creating the pits of Utumno, where he takes as many races as he can and personally enacts hideous, unspeakable tortures upon them until all that remains are grotesque perversions that he can use as his servants, ruined terrible forms of life. Morgoth proceeds to destroy the world trees, and betrays and murders the king of the Noldor elves, stealing their treasures from petty greed and leading to the deaths of many thousands of elves when they pursue him. Once he sets up his base of operations in Middle-Earth, Morgoth launches campaigns of conquest. He delights in corrupting men into darkness, manufacturing and playing off corruption in their hearts to set them against eachother and their allies. Morgoth launches brutal campaigns of slavery and genocide, and is responsible for the destruction of Gondolin, the most beautiful and proud elven city, with full orders to exterminate civilians who are saved solely by the heroism of the city's warriors. Entire regions pretty much cease to exist with their inhabitants enslaved or wiped out, or taken for horrible deaths. Morgoth is also unique in that he's an attempted rapist, trying to rape the elven princess Lúthien out of nothing more than cruel lust. Morgoth ends with no redeeming features whatsoever. An evil god, genocidal conqueror, brutal overlord, corrupter, Morgoth fits it all. At one point, he condemns a man to horrible torture and then enacts a curse to see his children grow, suffer horribly and be rejected by both life and death, solely because the man dared defy him. There is no act too evil or petty for Morgoth. He commits atrocities on the petty personal scale, and on a grand, worldly scale alike. He horribly tortures prisoners for the sheer fun of it. And his ultimate goal is to destroy the universe out of spite and jealousy that it was created by God instead of himself, and he isn't Almighty within it.
Darkness Induced Audience Apathy: The Silmarillion, in fleshing out the history of Middle-Earth, paints the picture of a world which is an irreparably broken shadow of its former glory that will continue to backslide until a Ragnarok-alike event in the far future. It's understandable if this colours your enjoyment of The Hobbit and The Lord of the Rings somewhat.
So does Morgoth. Apparently, he looks like The Woobie for some. There is even a major Russian fanfic, The Black Book Of Arda, that even was piratey published as a book, that retells Silm from Woobie Melkor's viewpoint.
Readers will tirelessly insist the elves are completley incoruptible and all their wrong doing can be justified. Obviously their genoicdes, child killing, refugee butchering, attempted rapes and stealing the Petty Dwarves land count for nothing. Those readers usually cite The Lord of the Rings more than The Silmarillion, and many who cite this work actually appreciate the more bloodthirsty brand of elves, being tired of the wise, angelic figures personified by people like Galadriel.
Ensemble Darkhorse: Nerdanel. The amount of fanfiction and fanart she has received is in no proportion to the very limited pagetime she has in the published Silmarillion.
Fëanor: He crosses it when he leads a shocking massacre of the Elves who dared refuse him use of their ships. Then he crosses it again when he sails to Middle-Earth with his most loyal followers, then burns the ships so the majority have to travel through the freezing far North, an ordeal where many of them die.
This has been the topic of endless debate in Tolkien fandom. Basically, you can argue that the massacre was unintended (Fëanor never gave the order to kill anyone), and those left behind after the ships burned could just go back to Valinor, since they were unhappy with the whole Flight thing.
Morgoth crosses this in the eyes of the Elves when he kills Finwë and steals the Silmarils. The moment that hits home just how evil this guy is, though, has to be the cursing of Húrin's family. Túrin's life was just one tragedy after the other, ending with his suicide. This is made even worse when you realize that all the misery was really caused by nothing more than Morgoth's temper-tantrum. Especially since Túrin wasn't even the one that provoked Morgoth; that honour goes to Túrin's dad. Túrin's miserable life is merely a decades-long torture inflicted on Húrin as punishment for his defiance.
Never Live It Down: Isildur. He actually performed many great and heroic deeds in his life, not least saving the White Tree and helping defeat Sauron. In fact, he's one the who actually defeated Sauron. Nevertheless the White Council (and real life Tolkien fans) remember him almost solely as the man whose hubris allowed Sauron to survive. What makes this especially unfair, is that no one could have done any better. In The Lord of the Rings Frodo is in the exact same position, and makes the exact same choice. No one can destroy the One Ring.
MORGOTH. The Satan of Arda, Morgoth engaged in Mind Rape without even having to think about it, and the only sort of pleasure he could experience came from horribly torturing and corrupting Elves and Men. In-universe, lesser Ainur were driven to insanity by his eyes.
Older Than They Think: "Earendel" is an old Northern European name for a god or a star or something along those lines. It seems to be one of those words that stick in peoples' heads : names like Earendel/ Horwendill crop up in the oddest places - James Branch Cabell and John Fowles's The Magus, and such.
Selfish Evil: Melkor stole the Silmarils and kept them from Ungoliant out of raw irrational greed, despite the fact that they painfully scarred his hands and burned all things evil that touched them.
Strawman Has a Point: Eöl, being one of the Dark Elves who chose to remain behind in Middle-Earth rather than sail West to the Valar, hated Fëanor and the Noldor who fled Valinor and pretty much invaded Middle-Earth, even going so far as to kill Elves of Eöl's kin. Thus he refuses to cooperate with Gondolin or the other Noldor states, and allies with the Dwarves and (presumably) the Green and other Dark Elves.
When Eärendil wanders through the streets of deserted Valimar and the dust of the gemstones covers his feet. Note that this was originally supposed to be much more of a Tear Jerker, as Eärendil had arrived too late and the Elves had already left for Middle-Earth; Tolkien changed it to make it a bit less tragic, with the Elves only being away at a festival and soon returning.
Jerkass Woobie: Fëanor, so much. He gets a lot of sympathy and apologetic fans for someone whose actions directly set in motion a series of events that led to so much suffering and death, including genocide and a world-shattering cataclysm. Possibly because, despite being a jerkass of truly epic proportions, he was also a total badass.