During the rogers-skinner debate, the most important difference between the two was over:

A big difference was their view of human free will.

B.F. Skinner saw psychology in terms of behaviorism, that our actions are shaped as reactions in consequence to environmental factors.  So the best way to promote healthy behavior is to shape the environment in society to cause our behavior to be turned in positive directions.

Carl Rogers believed in a person-centered approach to therapy, working with the person's internal thoughts and experiences.  He was concerned that Skinner's approach could lead to some level of cultural engineering, with some deciding how others' behavior in society should be shaped by controlling external factors.