I think it's because Vayne was a champ released in that weird Season 2/3 era where Lore was starting to get pretty rocky. She's one of the last champs, IIRC, to receive a Judgement, and unfortunately that Judgement doesn't tell us too much other than "wow Vayne's cool you guys" and she outsmarts summoners. Everything else about her backstory was "It's like Batman but with a witch."
That left Vayne in a place where, like a lot of champions of that era, fans were left to define her personality. So a lot of people got the impression, due to it being popular in fan works, that Vayne really was basically just Batman. She's serious, stoic, and wants to cleanse the world of dark magic. I remember a pretty good topic on the old boards regarding if Vayne would be hostile to Amumu, since while he is involved with some pretty dark magic, it's not his fault or something he's doing on purpose.
So, when the new lore filled in the gaps, and we learned that Vayne was less of a superhero and more of a zealot, a lot of people were upset over her character being retconned, although it really wasn't. That view of her was just so popular that it was basically canon in the eyes of the fans. Of course, that's not the only reason I think some people don't like it, and to each their own there.
Personally, I find her a lot more interesting now than I did when she was released, because she throws an interesting cog into the Demacian machine, and it also makes her a bit of a foil to Lucian, someone who has similar motives/goals, but seems to be much more careful about not being overcome with revenge, according to his actions in Shadow and Fortune.