Because it is better for some people for some games. I started on consoles, and as such, I am very comfortable with controllers. However, when I started playing PC games as well, the games were completely different types of games (adventure/platforming vs. 4X/FPS/RTS) and thus for me it mainly comes down to the genre, and even sometimes the game (and usually not the platform).
Interesting, I just remembered something before the 'standardization' of the controller. I started on an Atari 2600, which was mainly a joystick with 1 button (right hand on stick, left hand for button) and a paddle with no buttons. The jump to NES wasn't too big of a deal, but there was a slight learning curve switching hands, but definitely better to have 2 options for the button hand instead of just 1. But the jump to the SNES was a big deal; 2 buttons to 6 buttons was a such a HUGE jump, plus we had to use our thumbs AND fingers. It was hard enough to remember what buttons did what, but even the muscle memory takes time (I actually really hate Xbox for flipping the face buttons. B is on the bottom, not the right

). Then, holy shit - N64 controller - where do you put your hands?! Will we need 3 hands to play this right?! Since then, the controllers have become pretty standard, the last real innovation was the analog sticks and now all basic controllers are some variation of the GC/PS2/Xbox setup with 2 analog sticks, a cross-pad, 4 main face buttons, and 2 sets of 2 shoulder buttons. (ok, they have motion, but still pretty underused) (oh, the Wii/Wii U still use them, at least the classic controller, pro controller and Wiipad all do).
Point is: Controllers have became standardized, but it used to be that you'd have to learn each new one. Now it's pretty much pick up and play no matter what system, just what do you prefer. K+M, you just learn WASD and mouse and you're generally good to go - and it's been that way for even longer. Learning how to type helps though for key location memorization.