There is an important difference:
Apply to [something] refers to submitting an application for something, such as a job, school, or program. Source.
So, that would mean that "apply to its communications program" would imply that students will submit an application to join the program.
On the other hand, applying [something] means to put it to use especially for some practical purpose. Source.
Therefore,"apply its communications program" would suggest that the students will use the program.
Now, as the goal is to increase the number of listeners, I would guess the correct option would be "apply its communications program", meaning the university will encourage students to tune in to the broadcasting to boost numbers and reach such a goal.
Hope that helps!