I can't speak for all programs but I know in my SW program it is definitely a safe place, our school prides itself on being an ally and we have had guest speakers come (who were trans) into our class room to talk about their experiences. For me, that was the most eye opening experience because I had never known anyone trans.. Sorry going off on my own personal experiences. I think that in most grad programs people are older and more mature and would not judge or create an unsafe environment for a transgendered person. It should be based on the work that you do.