The problem is that it's sites. Not servers. More IIS boxes are 1-site and 1-app boxes. For instance, GoDaddy parks 10,000 domains on one instance of Apache. In fact most domain companies park incredibly large numbers of domains on one server, which skews
the results completely.
I think Netcraft also gives figures for
active domains, a little further down the page. Taking this figure, they reckon that Apache stands at 47% and IIS stands at 37%