On Tumblr and Twitter Swan Queen fans are very upset, tweeting messages to the shows creators saying "I'm not intentionally saying this. Fuck You." The Swan Queen ship is one of the most vocal in the Once fandom, and have accused non-shippers of homophobia. This post, resulting from when one of the show actors stated that SQ wasn't going to happen, is a good example of some of the things the fandom says.
As a Once fan, I do NOT get Swan Queen as a couple. Both characters have had exclusively heterosexual relationships, they are constantly at odds, and the Queen tried to kill Emma at least once. That doesn't necessarily mean they can't get together. Spike and Buffy happened so anything is possible! But I never saw the obvious signs that the SQ shippers did.
What I did see was the potential for a different show. Emma is the biological mother of Henry, a child she placed for adoption. Regina is Henry's adoptive mother. Emma and Regina both are emotionally damaged people. Emma was separated from her parents and believed she was abandoned. Regina's mother killed her fiance and forced her to marry a man she didn't love. A lot of the fandom stories stripped away the fairytale background of the series to focus on a modern world where two mothers try to find a family with each other. That's what SQ fans want.
It's just that they are trying to find it in a series that is all about the fairytale background.
I can't speak about the difficulty of not being represented in the media. I'm a cis, white, straight, female. I have plenty of characters that represent me. I might hate what that representation is much of the time (like in rom coms) but I have Kitty Pryde and Veronica Mars, and the cat lady from The Simpsons. My grandmother was the daughter of Polish immigrants in a poor Chicago neighborhood. She used to tell me that she was so excited to see any movie where the brunette wasn't the bad girl. She wasn't going to see someone who looked like her or lived like her, but she took her media representations where she could. Some GLBT have told me of similar things in their own life. They didn't have shows that really represented their lives so they'd watch Saved by the Bell viewing Zach as being gay and hooking up with AC Slater.
And even though there is more queer characters in the media now, they still are not representative to the whole community. Finding representation where you can still happens. Sometimes shows take advantage of it and intentionally play up the subtext in order to get LBGT fans to tune in. This is called Queerbaiting.
That Feminist Dyke has a great overview of Queer baiting, although I disagree about the idea that Sherlock started Queer baiting in the first episode. I felt that the "we aren't a couple" was an attempt to make it clear to fans that they weren't going to be a couple. This is because many of the modern readings have included the homosexual context (such as The Private Life of Sherlock Holmes). I do believe that by the second series the show was queerbaiting, possibly because the talk about them not being a couple didn't stop the world from shipping it anyway.

Anyway, Queer baiting is a thing. It's a real thing and a real problem. Rizzoli and Isles admits that they play up the lesbian subtext even though they don't plan to ever have the girls set together. This was their promo poster for a news season.
The Once statement at SDCC seems to be the opposite of Queer baiting. It's officially not happening. To be fair, there were plenty of reasons to not think it was going to happen before now (like the statement of other writers and actors on the show and the fact that they keep trying to murder one another). And yet people are furious with the series in a way that I haven't seen people angry with Rizzoli and Isles. They are hurt that the show has ruined their ship. I shipped Marian/Guy from Robin Hood. I know about shows killing your ship (literally). But I just didn't watch the final season of the show and went into fanfiction world where they lived happily ever after. I didn't tweet threats to the producers.
But then again, Marian and Guy were a ship for me, not a representation of me. It's natural for SQ fans to be more upset. Still, I don't know what shows are supposed to do when they find out about GBLT fans who are finding unintentional subtext in their work. If they play it up they or continue they are Queer baiting. If they come out and say that it isn't going to happen then they are accused of being homophobic (because they don't come out and state that other non-canon ships aren't real) or killing the ship.
The answer, of course, if to have more representations of GLBT characters and relationships so that people didn't need to search subtext for characters that they relate with. Of course, that comes with its own set of issues I'll have to write about one day. I will point out that it is hard for me to agree with the charges of Buffy playing into the dead lesbian cliche when EVERY couple on the series met an unhappy ending. If they allowed Willow/Tara to be the only couple to be together it would be awfully paternalistic and pandering of the series.