I would imagine that it is because they are very close to some people that are trans. I think it must be a horrible situation, in a highly gendered society, there is no easy fit for them.
Really, though, the argument, as I see it, is in the solution. The feminist choice would be for an equal society where women (and men) are free from patriarchal oppression. Gender would cease as people, of either sex, would be free to express their sex without conforming, in any way to gender stereotypes.
The solution we, as a society, seem to be gravitating towards, currently, seems to be to let people declare their gender is opposite to their sex. However, this of course, problematically, reinforces traditional, oppressive sexual stereotypes. Which adds to the problem.
I think the confusion arises in vociferous argument. The contention begins when it perceived that feminists have no sympathy regarding the problems people face, when they don't fit sexual stereotypes. When, really, I think, where we differ is the opinion on what the solution should be. Yet, it is hard because sexual stereotypes, within society, will not be changed overnight. Until then people will suffer oppression.