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It's totally relevant. Trans people experience attacks at a much higher rate than the background population.
I would really love to live in a world where Chelsea Manning's transgender identity and her very public transition would not affect how much some people might vilify her. But there are many people that are still very uncomfortable -- violently uncomfortable at times -- with transgender people (and generally people with non-binary/fluid gender identities).
Further, Manning's transition was very public, and her transition was likely for many people the first time we/they read a newspaper article or heard a news report that used a different pronoun for someone than they had previously. For people new and resistant to the idea, that might breed resentment.
Manning is not merely a transgender person, but a very high-profile transgender person. I think that this, by itself, and separate from her still-hotly-debated role in leaking classified material, articulates significant dangers that she faces in returning to civilian life.