My first thought on this is, how did they explain women who wanted to be men? It's not something I want personally, but I first became aware of Gender Dysphoria and transgender issues through a female friend with a long-held discomfort with her gender. And I'm reasonably positive she's not alone in the world in this, but that particular theory seems very centered on men who want to be women. Am I missing something?
Between 25% and 50% of transsexual people are trans men. But transphobes prefer to entirely ignore their existance. This mainly seems to be because transphobes don't actually know any transsexual people, and instead base their opinions on television shows or something.
Anyway, I'm sure that was a major factor in discrediting that theory.
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On the separate subject of LGB groups that discriminate against trans people, they're largely the minority now.
A few of the big groups really screwed up in 2007, by supporting a Federal Employment Non-Discrimination Act that specifically excluded trans people from protection. They thought it might help the bill get passed, because we were yucky freaks and maybe the straights would accept them if they distanced themselves from us. Instead, the bill still got rejected. Even worse, it set an explicit precedent that state/local anti-discrimination laws for gay people did not apply to trans people, forcing courts in some areas to take rights away from trans people.
But most of them apologized and swore they'd never do it again. ENDA 2009 included gender identity as a protected category. The Advocate did run a poll asking if members would support removing trans people from ENDA to try to get it to pass (obviously angering some trans people), but the overwhelming majority voted against it. And even Stonewall UK, which is one of the only big organizations that explicitly does not include "T" in its acronym, ended up backing down from giving an award to Julie Bindel, who has written some extremly transphobic things in the past ten years.
Most transphobia you'll find in groups who can't spell "Women" generally originated with a certain subset of radical feminists in the 1970s. These were generally middle/upper-class white women who didn't care about working-class women or non-white women. Many also believed that orientation was a choice, and "chose" to be lesbians.
They're still the boogeyman for some people (mostly on the far right) to point to when talking about "Feminazis." But the funny thing is that a huge percentage of them actually realized (duh) that orientation isn't a choice, announced that the evil lesbians had corrupted and molested them, joined the ex-gay movement, supported Prop 8, etc.
Some of the others, who actually happened to be lesbians, have started writing in far-right journals. Pro-Prop 8 pastor Rick Warren actually used them as examples of people he'd work with to undermine things he believed were immoral (pornography, in this specific example), and that's not exactly a ringing endorsement for anyone in the LGBT community.
So really, they're not representative of the greater lesbian community. Few of them are under sixty years old, so it doesn't seem like they were successful in recruiting anyone from younger generations.