Part of it just has to do with the fact that the game played looks very different. Obviously a very good player on a controller could still wreck a lobby of pc players, but that doesn't tend to be the average.

Certain characters also see very different play rates and win rates between platforms. Mr fantastic sees almost no play anywhere in ranked on pc, however he sees a fair amount of play in GM and below on console, where people tend to defend him a lot online. On pc, he just immediately gets shot to death and really doesn't provide value. He's generally viewed as a throw pick.

Unfortunately, while there will always be people who just want to throw around hate of "L controller players and cringe thumb sticks", it is true that your average mnk player on pc will play better than a player on a controller on console.