They're actually supposed to be anti-protons, part of the building block of matter. Since he's Superman, that doesn't do to him what antimatter does to normal matter, which is to blow it up, suicide bomber style. It was a very silly comic book science sequence, like all the Marvel Comics characters who use "dark matter" and "dark energy," which is depicted as shadow stuff.
(Dark energy and dark matter really just means "unknown" types of energy and matter, because astrophysicists don't seem to realize the rest of the world will run with the most literal popular interpretation of things. While we don't know yet for sure what either is, they're probably just energy or matter that's imperceptible to us for one of a number of regions, and not intrusions from a spooooky netherworld.)