So are you saying that IIS is fine for hobbyists, but when real work needs to be done, real professionals use Apache or Nginx? That's what your argument amounts to.
Many, many, registered domain names don't exist as real web sites. Instead, domain name speculators ("domain squatters") buy them and hold onto them, hoping to sell a "valuable" name to a real business at a huge mark-up. These names don't need a real associated web site since they won't receive any traffic unless someone types a domain name into their browser incorrectly. They can just exist as a database entry in an old server that serves up a default template with some ads and a "this domain name for sale" page.
There were reports a number of years ago that Microsoft was occasionally paying domain name registrars to put these unused sites on IIS as a marketing wheeze. There wasn't a lot of money involved, but it's not an expensive service to run. Hence, this is why "all sites" numbers go up and down like a roller coaster, while "active sites" and "top million sites" numbers changed relatively slowly and in line with well known industry trends. The "active sites" has just one "bump", which I believe is from when Netcraft had to start accounting for this phenomenon by testing if a site is a "real" site.
This is why the "all sites" numbers are meaningless. They don't have any correlation to how many web servers or real web sites actually exist. Compare the "active sites" numbers to the "top million sites" numbers though, and the relative rankings are the same, and the market share numbers are roughly in line (although "top million" trends tend to lag "active" obviously, as the biggest sites have generally been around for a while).
If you're a server administrator or web developer and want to know what new skills you ought to be working on, then the "active sites" numbers will tell you what you should be paying attention to if you want to address the widest real market.