The chart shows a steady decline from the early 90s into the 2000s. Something is missing. There's no way that cyberpunk is falling out of favor here. The article suggests that perhaps the fall occurred because we are living in a highly technological world now and much of what was once considered SF might not be so anymore. I think this is only the crux of the matter, but we'll address that first.
Our definitions of cyberpunk are changing, unfortunately, and as we become more and more technologically inclined it will continued to change its meaning. However, even if something ceases to be SF doesn't mean it can't be called cyberpunk. Many technothrillers could very well be cyberpunk novels, even if nothing necessarily 'new' is presented. Cyberpunk isn't as restricted by a time frame as space operas. I would say that there is probably a lot more cyberpunk out there than we realize. We just don't know it because it's not labeled as such, and since we live in a society that is constantly advancing, our definition of what makes something cyberpunk is changing and the line between that and normal technothrillers becomes very fuzzy.
However, another issue with the argument, which is nothing against the io9 folks, as they did do a hell of a lot of homework to have to find all the things they did find, which would have easily taken hours, is that it seems we're paying attention to a primarily English language market. What about China? China is the home of the world's largest circulation SF magazine and their market for SF works is exploding. They eat it up like crazy there and some authors actually make a living having works translated and sold there. There is Russian SF too, which, while focused a lot on the uses of governmental failure and dystopic themes, does deal with cyberpunk elements from time to time. There are dozens of countries out there contributing to the global market of SF. There has to be a myriad of cyberpunk books and movies in such countries. Technothrillers are a big deal, and so are cyberpunk novels, even if you don't think of many of them as cyberpunk. If cyberpunk is, in fact, seeing a significant decline in the U.S., that doesn't mean it's seeing that decline elsewhere. Some countries are significantly behind us as far as SF goes, and so they may just now be exploding with new cyberpunk themes. We should be paying attention and translators should actively seek to bring these works to the American market.
One more issue with the argument is that so many SF works have cyberpunk elements built into them. This should say something about cyberpunk as a genre. It is unavoidably important! It has built itself into the fabric of SF and as long as SF keeps it around it will never die. This goes along with the notion that just because something isn't labeled cyberpunk doesn't mean it isn't cyberpunk. Cyberpunk isn't really going to go anywhere. It'll probably become full reality and then it won't matter what we all think about it anyway.