It is by design.
An airplane have three axes to move, unlike a car, more controls should be provided to the pilot. As primates have two legs and two arms, the designers of airplanes put foot pedals to control rudders.
Because Newton came up with the first law of motion before airplanes were built, we needed to have devise a way to stop airplanes, and hence brakes were invented. But unlike cars, where a foot or feet are used to apply brakes, rudder pedals were already occupying that region. And hence airplane designers added brakes on top of rudder panels.
Like everything else, this also evolved overtime.
The rudder's direction in aircraft since the "Golden Age" of flight
between the two World Wars into the 21st century has been manipulated
with the movement of a pair of foot pedals by the pilot, while during
the pre-1919 era rudder control was most often operated with by a
center-pivoted, solid "rudder bar" which usually had pedal and/or
stirrup-like hardware on its ends to allow the pilot's feet to stay
close to the ends of the bar's rear surface.
I disagree that by combining them leads to any confusion. The rudder pedal/brake assembly is very easy to understand and master. The mistakes you make as a student are minimal and do not happen after a little training anyway.
Another reason for having rudder pedals on the floor is that in a coordinated turn, you might have to add slight rudder along with banking the airplane. As hands are used to bank, rudder pedals are controlled by feet. This situation is only applicable during flight.
During flight, brakes have not any effect as they are applied on main landing gear.
During taxiing, when you press the rudder pedal (not applying brakes), the nose wheel is turned (smaller airplanes).