"Queer" is a reclaimed slur* against LGBT people specifically. I think it's discomfiting for members of the group that once used it a pejorative for LGBT people while treating them as lesser to use it to describe themselves, particularly since so many do so specifically to try to identify out of being straight. It's not as bad as white people using "n--a," but it has the same valence.

*Of course, there are also many LGBT folks who still view it as a slur, because they've had it used against them in that way. Imagine the straight chick who derisively called you "queer" in high school declaring in middle age that, despite only ever having heterosexual relationships, and marrying a man, and benefiting her whole life from presenting and living as straight, she's "queer" and belongs in LGBT spaces with you.