Protomatter, while being a strained plot contrivance, was nothing more than an excuse for Genesis not working. It, in and of itself, wasn't a Maguffin upon which the very premise of your script rested, which is why we can take it a bit better.
Even Genesis itself, while being the plot mover in TWOK, wasn't the actual plot. This is largely because the movie was really a character piece about Kirk with Kahn being the force of nature to show us Kirk's fallibility.
Red Matter was just another plot device, very similar to the ones used in the recent movies (THORION RADIATION!). The problem is that the plot itself hinged on this magical substance, from the set up to the overall threat. Since the Red Matter was thrust into the foreground much more than Nero himself, it got a lot more attention.