Call it whatever you’d like. Phlebotinum. Kryptonite. The X-Gene. Nanotechnology. Unobtanium.
Red matter is... the stuff that explains the science fiction in your story. Or, rather, the stuff that refuses to explain anything and just excuses the science fiction in your story. A single source origin story for everything impossible that you want to include, no matter how disparate and bizarre.
Do you want to write about an invisible woman this week? Well, lucky for you, the Hellmouth makes some people invisible. What about a demonic computer program? Hellmouth does that too. How about kids becoming hyenas? Still Hellmouth. What about?—Hellmouth. And?—Hellmouth. Bu?—Hellmouth. Hellmouth. Nothing but Hellmouth, all the way down.
Personally, I think red matter is great. It does away with so much exposition and moves the plot along. In the seminal novel Frankenstein, Mary Shelly skips blithely over how Dr. Victor Frankenstein animated his creature (with an off-hand, “No, no, it is far too dangerous for you to know,”) and gets right into an allegory for God’s relationship to Man. Even when James Whale’s later movies delved a little more into the how, it basically stopped at lightning and “chemicals.” Which chemicals? The ones that worked.
Yes, some really great science fiction is about how the impossible is happening in this story, particularly the works of Jules Verne and Isaac Asimov. Chris Roberson’s iZombie has a brilliant single origin for zombies, vampires, ghosts, poltergeists, werewolves, and possessions, involving the ancient Egyptian belief in over-souls and under-souls.
But most science fiction isn’t really about the how. Most is about why we want the impossible to happen, and what the consequences are if it does. Wells, and Orwell, and Bradbury, and L’Engle used the impossible to comment on society, and government, and family, and love, and used only the barest explanation of how any of this was done.
And the red matter in Star Trek (2009) is my favorite example of just cold not explaining anything. First off, it does not try to hide the fictional nature of the substance behind a scientific sounding name. It’s not a dilithium crystal. It’s fucking “red matter.” (Ironically, in giving it a dumb name, it sounds more like real scientific concepts like dark matter and the Big Bang.) Secondly, red matter is a big ball of red... let’s say paint? That makes black holes. That are also sometimes wormholes into an alternate timeline. Why? Because that’s what the writers needed it to do.
Obviously, any thinking about red matter will find faults with it. Any thinking. At all. If the wormhole spat out two ships, why didn’t it spit out the energy of the galaxy destroying supernova it was created to absorb? Why does a little amount destroy a planet, but the great big ball destroys only one ship?
But the Star Trek franchise is full of red matter. Transporter accidents. Holodeck accidents. Warp speed accidents. And that’s not getting into the series of Omnipotent Space Douches who show up just to rewrite the laws of psychics on a lark.
By calling their plot device “red matter,” the writers basically held up a neon sign that said, “No. Stop. Don’t think about it. Abandon all disbelief ye who enter here.” Just accept that it works like we say it does, sit back, relax, and enjoy shots of Chris Pine hanging from things. (Seriously, he does that a lot. A drinking game involving that and lens flare will kill you.)
I wrote a post about why I hate X-Men’s mutant gene, and one of the reasons I hate it, besides it undermining the metaphor of the X-Men, is that it explains too much. You could just say “they’re mutants” and move on to Wolverine bitching at Cyclops, and it’d be fine. But instead you get bogged down in how the gene works, and how it gets passed on, and why it causes this mutant to be big, blue, and furry, and that mutant to turn into ice. But really, the entire Marvel universe can be explained by “Cosmic radiation hit the Earth that one time, and that’s why things are weird.”
In short, it does not matter how Superman flies. It only matters that Superman can fly, and how he chooses to use that power. Unless there is a really good story there, getting into the how of the impossible is just... hand-waving.