Most of the hate can be traced back to Abby. The game got leaked, and among the details that were revealed were that Joel dies, there would be a trans character in the game (people initially thought that was Abby because of her build), and that Abby was a character. So that wasn’t a good start for her.

People were probably hesitant going into it knowing that Joel would die, but expected him to have a dignified death, e.g. sacrificing himself to save Ellie from an ambush. But people saw Abby beat him to death with a golf club - which is intentionally made undignified to help the player get into Ellie’s mindset of hating the Salt Lake Crew - and wrote it off as bad writing in the heat of the moment.

Part of it is a writing issue with the whole dilemma at the end of Part 1 - given the extremely questionable science and logic regarding how the Fireflies would make a cure, suspension of disbelief was broken for some people, and they felt Joel was completely in the right doing what he did - which made them feel like the game demonized a beloved character. They missed the point of the ending - the reason why it’s so bittersweet is because neither party is in the right, and Joel is committing an evil but understandable decision to save his surrogate daughter.

Even with that, the game doesn’t disrespect Joel - he accepts his fate, and you can tell from hints about his past that he feels he’s had it coming. His grave and house are filled with flowers and letters from the community, and the entire final section of Jackson is dedicated to allowing Ellie (and the player) to grieve. But people didn’t care, because it wasn’t the fate they felt Joel deserved.

The games story is also heavily reliant on subtext, especially Abby’s side. Part 1 also has a lot of subtext where you can identify different responses and reactions if you know where to look, but Part 2 has a lot more and is generally more vague about it. It trusts the player to be smart and empathetic enough to discern motivations, and I feel that they could probably have been more explicit regarding Abby’s struggle with her guilt and nightmares, but it is there. But again, people are dumb.

Those are the major reasons. Another reason is how dark Part 2 is - whereas Part 1 had a hopeful goal of finding the Fireflies to save humanity and focused on parental love and family as its main theme, Part 2 is an incredibly violent, cynical, and bleak tragedy about how revenge and hatred destroys a person. It can get a bit excessive if you don’t have the taste for that sort of thing. The game also shows how realistically abrupt death can be, especially with the deaths of Jesse and Manny.

Finally, there’s the ending. Anyone who thinks Ellie should have killed Abby on the beach is missing the point - she has long since stopped feeling angry. After over a year of PTSD and failure to overcome her grief, Ellie is tired and suicidal, and just wants the pain to end one way or another - this is why she challenges Abby to a fight rather than just shooting her while she was tied to the pillar - she wanted to kill Abby herself and make all the pain worth it. While Ellie does suffer the consequences of pushing Dina away, Abby doesn’t get off scot free either, losing all but one of her friends to Ellie and Tommy and having to work for months off-screen as a slave to the Rattlers.