As others have pointed out, your premise is flawed. Some karateka are good with their hands, some are good with kicks, some are good with both ... and some are crappy with both. I wouldn't say that karate as a whole favors one over the other, although individual karate styles or practitioners might.
From a Western point of view, I can see one factor which might lead some casual observers to make the mistake of thinking karate was better for kicks. We have, in Western boxing, a native, highly advanced system of punching which is widely practiced from casual practitioners up to world-class professionals. We don't have such a widespread tradition of kicking in the West. (There's Savate, but it's not so widespread and it comes from Chinese origins anyway.) As a result, some Western observers might be impressed on a gee-whiz level with karate kicking, but not so much with karate punching.