UPDATE: The HRC sent out a press release regarding this incident. Jerame Davis at the Bilerico Project writes what I think is a pretty respectable overview of why their press release does not seem to match the actual situation; be warned that he falls into the trap of trying to defend the HRC from the side.
From the Tumblr blog "Get Off My Runway" I found out that representatives from the HRC at the Supreme Court protests told a group to take down a trans pride flag--twice--because transgender issues have "nothing to do with marriage equality." First allow me to state the obvious: These activists were not asked to take down their flag because it was irrelevant. They were asked to take it down because of shady gaycentric PR.
In other words, the HRC is chronically wary about allowing transgender people any sort of "spotlight" because they're afraid of how it's going to make the rest of the movement look to include trans people in a full role. The HRC (as well as many pretty-high-up homosexual-and-homo-friendly legislators and personalities) is very mainstream-targeted and intentionally goes with the least controversial path whenever possible. If you remember my essay on HRC logos and how sick of them I am, you'll remember that my semi-closeted friends used those to mark themselves because there's nothing overtly gay, queer, or LGBT about them. While this isn't inherently a bad thing, when it comes to the HRC it's a chronic assimilationist tactic. They are interested in an extremely mainstream agenda and it leaks through nearly every scrap of their advertising.
Although transgender people are also becoming much more socially acceptable (with the public transitions of several small children as well as celebrities like Chaz Bono), when the HRC looks at a campaign and tries to figure out how to make it more palatable to the mainstream, the first group of people they'll cut from* the team are transgender people.
For example, when ENDA was being debated, the HRC went with the stripped-down version that cut out trans people wholeheartedly because that's the sort of mindset they readily take: If kicking trans people out of legislation will get Paul Ryan to support it, then kick away! Similarly, when "Don't Ask, Don't Tell" was repealed, almost nobody mentioned that transgender people are still largely banned from the United States military, because advocating for that might creep people out. So the idea that having a transgender display of pride at a marriage-based event is going to disgust an otherwise pro-same-sex-marriage person is pretty standard HRC behavior.
But let's talk about something that the HRC reps at the beginning of this post said about transgender people and marriage equaltiy being two entirely different animals that should never interbreed. Is that even true? Spoiler alert: No.
When it comes to relationships, even heterosexual trans people often have a sort of gay stigma attached to our relationships, and based on our level of legal transition we may be legally considered in same-sex partnerships even when they are actually heterosexual. In my state, for example, I cannot legally marry a woman, even though I am a man--it says so on my license and everything. I can legally marry a man, but I'd have to out myself in every step of the process and as soon as I get court documents proving I've had surgery I'd only legally be able to marry women.
It's even more complicated when it comes to divorce; exes with vendettas against transgender partners have in the past tried to argue that their marriage was a same-sex marriage and therefore not a legal marriage, such as in the case of Michael Kantaras. He and his wife divorced and had a custody battle in which his ex-wife argued that their marriage was a same-sex marriage and therefore wasn't legal (Update March 29th: Thomas Beatie is having a similar problem right now; his divorce is being stalled because people are arguing he "wasn't legally male yet" when he married in 2003). Christie Littleton had her marriage voided by the state of Texas when she tried suing for medical malpractice on behalf of her dead husband. Nikki Araguz also had her marriage declared an illegal same-sex marriage after her husband died and his family sued to keep Nikki from inheriting his assets.
While cisgender same-sex couples deal with trying to get into marriage, transgender people have been fighting the same battles with more immediate effects at stake. To punch trans people in the gut even further, mainstream LGBT news outlets have even presented transgender opposite-sex marriages as same-sex marriages when it suits them, like when Kimah Nelson and Jason Stenson got married in New York.
Why do trans people appear to care less about marriage, then? Because although it certainly affects many of us, it affects us less than many other issues. Lack of solid employment opportunities, inadequate access to inclusive health care, being targeted by policies that criminalize normal activities that just happen to be performed by transgender people (like having sex or taking a piss), the number of youth left homeless, these are things that may make transgender people less likely to target marriage as the flagship goal. In fact, it's daily access issues like these that also cause many cisgender people to criticize the marriage über alles method for achieving equality.
And that's not even counting people like me, who maintain that the ultimate goal should be for total relationship equality and human rights--rather than legal marriage which would simply elevate same-sex couples without dealing with the problematic nature of the institution.
The really shady part is that the HRC, the Advocate, and other mainstream gay and lesbian groups and publications are extremely supportive of trans peoples' money and perfectly happy to latch on to stories about us that fit their agenda. So they see no conflict with supporting trans people just enough to get people to make donations before totally throwing us under the bus, or with guffawing about New York marrying a same-sex couple when a trans woman gets married to a man. I mention this because throughout this whole controversy I've seen people post links to HRC pages that are oriented toward transgender issues as if this means they are actually supportive... the reality is that they do this to keep people from criticizing their lack of concern for transgender people, not because we're actually a part of their agenda.
But to conclude, remember that creating a rift between "gay and lesbian issues" and "transgender issues" creates a false dichotomy. There is far more overlap than there are distinct issues between us, regardless of how often trans people are excised from them.
* -- Notice I said "cut from." The reason transgender people get such a
brunt of this is because many other groups represented in the community
were never a part of their agenda to begin with, like polyamorous folks
or nonbinary gendered people.