It's not that Pixar has always been good, like any company there's been ups and downs, but because Disney themselves have also gone all in on 3D animated films[0] (and none of those really come close to what Pixar puts out; even the recent flop of Elemental is still a better movie than most 3D Disney movies of the past decade), all those movies get compared to each other in a much more direct manner.
Back in the early 2000s, it was pretty straightforward; Disney did the 2D animation, Pixar the 3D animation. It means that when Pixar or Disney puts out a stinker, its easily covered by the other. A sort of trade if you will.
Disney has kinda now ended up in a bit of a slump for the past decade (likely directly the fault of the Live Action Remakes they keep doing - it feels really uncreative), so the highs and lows of Pixar are that much more apparent.
They'll be doing fine. Elemental sucked, but it doesn't seem like it's a pattern for Pixars movie creation process. Not in the way that Shrek's poop humor ended up dominating DreamWorks for over a decade or how Despicable Mes "marketability" ended up ruining Illumination.
[0]: The last blockbuster 2D animated movie was the Princess and the Frog and according to Disney it didn't make enough money to continue making them.