Windows doesnt have as much of a Web Server share as you might think. More and more servers are using Linux Distros.
That being said i think you are getting confused cause C# is used mainly for desktop applications. Not for WEb stuff. That is HTML, Java, PHP, Pearl, XHTML, Ajax and so on. C# and .NET are used for stuff that you use within Windows on your desktop. Not so much what you use on the web unless you are developing for use with Silverlight.
Dont take my word for it as i have not been in development at all. But from my understanding this is what i know.