Your code, as written does not make much sense. You define controller C, but then do not use it, and instead just use unity gain when computing closed-loop response. I am also not sure why you are mutiplying sys_cl by 0.25 when computing the step reponse.
The more meaningful code would be:
s = tf('s');
P_ball = 0.48/s^2;
C = pid(Kp,Ki,Kd);
what you see then is the angle of the motor (the variable you control). The output of the PID would be something like a voltage request to the motor. Another issue is that typically a motor transfer function is not a double integrator, like your plant transfer function, but that's for you to figure out.