When Glee was conceived, it was meant to be a show promoting acceptance and diversity.
Recently, a storyline was introduced with a character named Unique, who is a transgender woman. From the start, she has experienced transmisogyny (transphobia directed specifically at trans women) from almost everyone on the show. Some of this prejudice is presented as a joke. Transmisogyny is not a joke. Transgender women, especially transgender women of color, are overwhelmingly the victims of hate crimes against the LGBT community. In fact, the National Coalition of Anti-Violence Programs found that 44 percent of hate crimes against LGBT individuals were perpetrated against transgender women, overwhelmingly against transgender women of color. It is alright that Glee is showing discrimination, as this is a reality, but it should never be presented as a joke. When Unique's pronouns are not respected or she is called a man, Glee should make sure to present this as an unambiguously bad thing, instead of leaving such actions in a grey area.
In another incident of transmisogyny by people working on Glee, Dean Geyer (https://twitter.com/geyerdean) who plays Brody on Glee recently tweeted calling a person who criticized him a slur against trans women. When called out, he refused to apologize, and even said that he believes that the word is not derogatory. He eventually apologized for offending people, but not for his actions, and never admitted the seriousness of what he did.
A screencap of the exchange can be found here: http://media.tumblr.com/tumblr_mdcowe2zjs1qh6iw5.png
A screencap of the original tweet can be found here: http://25.media.tumblr.com/tumblr_mdcmg7rbVW1qb3re6o1_500.png
If Glee wishes to be an inclusive show that promotes acceptance, it must promote acceptance for all people, especially those who are most at risk of being the victims of discrimination. It must stop treating transmisogynistic comments as a joke, and must discipline those involved who publicly use slurs against trans women.