The reason behind applying the load to the central web is to focus on the deflection that occurs across the entire span of the I-Beam. This tutorial isn't concerned with the deflections that occur to the top and bottom flanges.
The problem focuses on the increasing impact which shear deflection has on shorter, non-slender beams. This shear causes a difference between the analytical Euler-Bernoulli solution and the 3D finite element model.
Note: If you have trouble selecting the correct surface body, select the main web of the I-beam and click on the central sheet of the multiple layers icon. The multiple layers icon along with the I-beam can be seen in the image below.