Pretty much all of it, actually.
1. They chose to base an attraction off of a film that was seen as problematic from initial release.
2. They then banned the film to try and make it go away.
3. The internet came into wide usage, at which point the knowledge that it was based on SOTS became more widely known.
4. Disney had basically the worst possible response. Rather than acknowledge it, attempt to educate people about the harmful depictions from the film, and give a content warning, something that has been done by Warner Bros. in front of Looney Tunes shorts, they doubled down and continued to bury it. The worst possible response.
Because nothing makes people on the internet more interested than forbidden fruit or banned content, this only causes the story to spread and mutate. And then the story becomes out of Disney's control because they did absolutely nothing with it. "Did you hear Splash Mountain is based off a movie so racist they won't even release it?!?!?!?" spreads around the internet and because it's not something legally viewable, people imagine it must be something akin to Disney's version of Birth of a Nation, even if the film, while far from perfect, isn't anywhere near that.
And the longer this continued, the more it perpetuated. Until it got to a situation where Disney felt it had no choice but to remove the ride.
It is pretty much entirely Disney's own fault.