Proton is basically a wrapper for wine with pre-installed dependencies for whatever program you want to run, often with specific fixes and settings for it, in its own instance/environment (usually with a separate C: drive and all those associated paths). It gets rid of the headache of trying to run all of it manually, but it's good to know how it works in case something breaks or you want to tinker with it, but even then there are programs to automate that process (like protontricks for those specific instances or winetricks more generally).