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.
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.