i am a cis woman but i have had a loving relationship with a pre-op trans-woman who remains a good friend. i can't speak for others in the poly community but i certainly wouldn't be trans-phobic and i would be very upset to think others were.
edited to add: i referred to her as pre-op only because that is how she identified herself at the time, and because she did go on to have surgery. i have friends who are trans who hate that term when applied to them because they do not plan to have surgery and do not identify as being pre- anything! full respect to them and to all of us in our diversity.