What's the big deal about the mouse and keyboard setup for FPS?

Try not to flame too hard :)
 
Anyway, recently got Painkiller off Steam and been enjoying it a lot. A nice return to old-school style FPS gaming.
 
However, I must say I really don't see the big deal about using a mouse and keyboard. I'm finding it very uncomfortable to use and cannot play for much more than an hour. I've never had any problems using a controller to aim nor do I have any problems using my mouse, I just find it extremely uncomfortable to use for long periods of time. 
 
What do you think?