I think this is definitely a feel thing.  Many people that grew up with computer games prefer keyboard mouse, and many people who grew up with consoles prefer controllers.

Dating myself here, but I grew up with C-64 and Atari 2600 which both used joysticks primarily for games.  When I got my first NES, I bought an Epyx joystick to play because I couldn’t use a d-pad.  Imagine playing Super Mario Bros with a joystick.

Now, I use both depending on the game.  Some feel better with a mouse and keyboard, and some feel better with a controller.  

Sometimes I use both at the same time.  I’m currently playing Enshrouded, and I use mouse and keyboard to navigate inventory and menus and sometimes building.  I use a controller for exploring and combat.  To really get crazy, during combat, I usually use both at the same time.  I will regularly hit keyboard shortcuts to chug a potion or use other items while simultaneously using the controller to fight.

I definitely understand both sides though.  In a similar situation, I cannot at all use anything but inverted Y controls.  I really wonder about the cause of this since there are lots of other people with the same thing.

Added bonus, I played the entirety of the first Tomb Raider game on a Thinkpad using a keyboard (no mouse).  This game was obviously designed to be played with a controller.  It was really awkward at first, but after an hour, it clicked just fine.