I personally have nothing against my T taking off her shoes. She has done so once or twice. My T and I have that type of relationship though..I take off mine a good deal of sessions and my T doesn't care. I asked her the first session I ever had with her though to establish that. We have also had sessions where we both sit on the floor instead of the chair/couch. My T is pretty damn awesome in my book for doing so and being so comfortable with me.

Since nothing was said from him to you when he took off his shoes and you didn't say anything as well he probably interprets it as okay to get that comfortable with you in sessions. I doubt he is trying to be unprofessional or make you feel weird. Since it does make you feel off about it you should bring it up next session. It is the beginning of a new T relationship that yall are establishing and comfort zones such as shoes being taken off. Nothing wrong with a little short discussion about it and moving forward from there! It may just feel too soon for something so comfortable to happen.