"Cf. La Cage aux Folles, Gemini, Angels in America, The Normal Heart, Torch Song Trilogy, The Killing of Sister George, The Boys in the Band..."
After Eight, of the shows you're citing, The Normal Heart and The Boys in the Band originally had off-Broadway runs, where they were indeed very popular but then again, so was Fun Home, which was sold out for the majority of its (extended several times) run. Off-Broadway shows don't have to draw as broad an audience, so the comparison to the Broadway production of Fun Home isn't really relevant here.
I would also argue that there are gay aspects to Gemini and The Killing of Sister George, those plays don't explicitly deal with LGBT subplots in the way that Fun Home does.
So, that leaves us with Torch Song Trilogy, Angels in America, and La Cage aux Folles. It should be noted that none of these plays deal with lesbian characters (or even have any lesbian characters, unless I'm forgetting someone in Torch Song), whereas Fun Home has a lesbian protagonist. Maybe it's splitting hairs to you, but I do believe that because theatre is often seen as the realm of gay men, not women, audiences are going to be more comfortable with a play featuring gay men than women. Not to mention, though there characters in La Cage and Torch Song are openly gay, many of them are drag queens and thus safely fit into old gay sterotypes that go back many years. I do actually agree with you that the original productions of La Cage and Torch Song were risky bets for their time, and that shouldn't be entirely discounted, but I don't think either of those shows force the audience to deal with gay sexuality in the way that Fun Home does- especially since Fun Home is not only about gay sexuality, but how damaging homophobia is.
Really, of your list, the only thing I think is truly analogous to Fun Home in regards to how daring it is with gay themes is Angels in America, and the original production, though obviously highly acclaimed, ran for about a year and a half, hardly any kind of smash hit, especially since the play was such an event.
In addition to the gay themes, I think Fun Home is also a difficult sell, despite the reviews, because it's partially about a suicide and takes place in a funeral home. There are many audience members who may not want to see a show, especially a musical, about those themes- I'll even admit being a little worried when an embalming scene was mentioned on this board, as that does make me a bit uncomfortable. So there's clearly reasons why the show is a difficult sell, but that doesn't mean that the audience is insulted by it. The (very full) audience the night I saw it lept to their feet when the show ended, so your thesis that the show is insulting to its audience doesn't really (nor has it ever) held water. It's insulting to you, but not to everyone.
I am a firm believer in serendipity- all the random pieces coming together in one wonderful moment, when suddenly you see what their purpose was all along.