As an educator, scientist, and science fiction writer, I often look at things from several perspectives. During my years of workshopping stories, I noticed that some otherwise good stories got some strong, negative reactions for reasons that had nothing to do with the quality of the writing, characters, plot, or setting. It had to do with theme.
You know, what the story boils down to in one sentence: love conquers all, good triumphs over evil, hard work pays off. That sort of thing. Anyone, well any writer anyway, can rattle off a dozen, no problem. We all know them and recognize them. They're the acceptable, society-approved ones. Turn them around (e.g., love is not enough), and you have your forbidden theme. Sometimes these can work to great effect, making for a surprising story, a memorable anti-hero, or something just a little more realistic.
More often the readers will just reject the whole story out of hand.
The first striking example of a "forbidden" theme I remember seeing in a workshop was at Clarion West in 1994. One of my classmates had written a fantasy story in which the central message was: once a slave, always a slave. Hoo boy, that didn't go over well. The critiques kept picking around the point that took people a long time to articulate, and that point so many wanted to make was that you aren't allowed to write a story with this message!
Of course, I'm sure such a story would have gotten a different reaction in a past society were slavery was accepted. Such a theme would have helped maintain the status quo, and would not have been forbidden. In fact, the story of a slave transcending their station would have been the forbidden story.
I've seen other forbidden themes crop up in workshops and elicit strong reactions, leading to members quitting, in fact, when they lead to critiques of the writer rather than the story. It makes sense. Critiquing the theme negatively is about as close to critiquing the writer as you can get. You have to say, "you're wrong to have written this. Your morals/judgement/insight are not what they should be."
Of course, if you can pull off a forbidden theme, it creates a very powerful story, and there is a range of themes that our society is currently two-faced about. Think about anything that splits society down the middle. Right now our politics split the country, and while I advise against writing polemic stories as they tend to be heavy-handed and suck, there are other things that go with our political split that are ripening now, especially for science fiction.
The extreme right of politics these days is associated with an anti-intellectualism that places faith above science, gut feeling above reason, and determination above preparation. Whether you know it or not, you get a steady diet of stories that reinforce these attitudes. The movie Armageddon, in which undisciplined but determined roughnecks replace well-trained NASA mission specialists to save the world, is one example. Star Wars is another, in which Luke is told to trust his feelings and put away his computer. More recently, the TV series Battlestar Galactica has been doing the same things, with Rosalin leading based on faith, and even the traitor scientist Baltar being turned toward faith over reason.
I'm using those examples from science fiction specifically for a reason. Science fiction, of all genres, should be the one pushing for reason! It's WORSE in other genres, where science and reason are regularly put down in favor of intuition and gut. Just think about every example of the determined American hero overcoming the criminal mastermind. Science fiction does promote the other side semi-regularly (e.g., the Star Trek episode where Kirk fights the Gorn in the arena, and can only win by using his smarts rather than his heart). "The Cold Equations" is another example, and not surprisingly one that has created strong reactions. Its theme is that ignorance of the laws of physics can and will kill you in a dangerous environment, no matter how cute and innocent you happen to be. That's a threatening message to a lot of people, who then feel compelled to pick it apart and point out its flaws rather than deal with the actual theme, which they would label forbidden if forced to label it.
I think we as a technological society, with myriad problems requiring science to address (e.g., global warming), need more stories with a few of these forbidden themes, and science fiction is the first place they can and should appear in larger numbers. If we're to have students really take to science and math they way we want them to, we need to change the messages they get daily from stories. We need to change the underlying memes of our society, and writers are the ones who can do it, or fail. I choose not to fail.