I think that the comment was a valid one.
We understand that you are aiming to keep the videos casual, but at the end of the day you are representing a larger entity than yourself. I don't believe that anyone is asking you to change how you work, nor the environment that best suits your needs, my office also bears a resemblance to a dorm room, however when providing a showcase for a product on which I am working, it would look very amateurish and unprofessional if I were to bring my intended audience into "my world".
I believe the point being made was a constructive criticism, to some the college logo is obviously a distraction, and since you now work for Microsoft and not your college, perhaps a Microsoft Logo might be a little more appropriate.
With that said ... great video, thanks for the insight and keep up the good work :o)