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I assume this is part due to many games only having support for OpenGL and DirectX, and no Vulkan support. OpenGL has the worse performance of the three, and DirectX is windows only.
But when you using proton, you are likely also dxvk, taking benefit of the optimizations made by game/engine developers for DirectX, while suffering little overhead from the DirectX to Vulkan conversion.
Also what do you mean as “runs better”? As in “better performance” or “better compatibility”? I’ll give you one answer for each question, but off course its not the only one. Other cases may have another explanation why the Proton version runs better. This is a complicated topic which cannot have a generalized answer for all games.
A lot of Linux ports are not the best quality to begin with, or even if they were good once, they’re out of date, utilising old fashioned technology that may not be the best at taking advantage of modern hardware. Conversely the windows version was often better built to begin with, and the translation layers have had a huge amount of effort put into them to make them as performant as possible and utilise as much of the hardwares capacity as they can, so much so that sometimes the proton version of windows games running on Linux is actually more performant than the windows native version on running on windows!