If you were in that situation, wouldn't you want to have a safe space to talk to people who understand? To not have to deal with justifying your identity to people? Is it really "intolerance" just to want a place you can feel safe?
Now as a cis person I have never had to deal with the issues described, but I can empathize. What you are saying makes abstract sense and would be fine in a world where everything was fair and everyone was truly treated equally. However, that's not the world we live in. I urge you to reflect a bit more on this.
Blatant hypocrisy will never help improve the situation, however. One group of people who complain about being ostracized when they're in the minority should not turn around and ostracize others when they're in the majority.
Banning people they disagree with from a rather public forum like a subreddit, for example, only hurts their cause and their reputation. It creates more animosity. Denying the basic ability of one to express himself or herself is just not justifiable.
There is a difference between "animosity from others" and outright hatred, violence and oppression. There is a difference between "animoisity" and being denied many of your rights and being locked up in a mental institution ( 11 yr old trans girl institutionalised: http://www.pinknews.co.uk/2012/01/31/german-trans-girl-to-be... ).
Banning people they disagree with from a rather public forum like a subreddit, for example, only hurts their cause and their reputation.
I disagree. I think there is empirical evidence that the LGBT or Trans rights groups have benefited from having safe spaces. Trans rights and LGB rights & politics have increased over the last two decades, in part I think due to more trans & LGB people coming out because they have safe spaces to explore themselves.
These groups do not "decry intolerance in all forms", but instead decry intolerance against people of different gender & sexual identities. Many (all?) of these groups have no problem not tolerating people who don't tolerate gender & sexual minorities. There is nothing hypocritical here.
Instead of banning the detractors, they should try welcoming them into the community, and maybe even try to understand them and their viewpoints better.
"detractors"? Are we talking about the same thing? This isn't some technical mailing list where the discussion is whether the programme should have lots of defaults or have lots of options for power users. The "detractors" want to kill LGB people. The "detractors" think that trans people can be assaulted and killed if (for example) a straight cis man finds a trans woman attractive.
These "detractors" do not come into the community to learn more. They aren't "detractors", they are haters. They come in with hatred, hostility with the goal to destroy the community.
And you think things would be better if these haters were allowed to say whatever they want in these communities?!
Instead of banning the detractors, they should try welcoming them into the community, and maybe even try to understand them and their viewpoints better. They may not change the attitudes of those with differing opinions, but at least they won't have made the situation worse by introducing more intolerance.