Dear Skan,
CST (and HFSS) are electromagnetic field solvers. For microstrip lines the waveport needs to be much larger than the width of the line in order to capture the fields so it can make the correct calculations. Try doing a parametric study of a microstrip line where you vary the port size. As the port gets larger you should see the port impedance converge to the theoretical value. A coaxial cable does not have any fields outside of it due to Gauss' Law so the wave port only needs to cover the edges.
I hope this helps.