Well, the reason you find the difference between the charges of Linux and Windows operating system is the fact that Windows is a licensed product and Linux is 'Open source' i.e. Free of cost

Hence, if you choose Windows operating system for your Dedicated server, you will have to pay charges for Windows operating system also but if you choose Linux operating system, you won't have to pay licensing fees for it which reduces the cost of Linux Dedicated servers
Now, as Linux Dedicated server is cheaper, everyone wants to go for Linux Dedicated server, however, if you have your sites developed in ASP, FrontPage, ASP.NET environment, Windows Streaming Media, Access, MS SQL Server, or any of the other Microsoft’s owned technologies then you should opt for Windows Dedicated servers
When it comes to Linux Dedicated servers, Linux operating system is compatible with most of the Software's, Programming languages (except ASP, ASP.NET etc.) and hence you can choose Linux operating system for your Dedicated server if you do not need ASP, ASP.NET or any of the Microsoft owned technologies
You can find more information about the 2 operating systems through the below link :
http://www.bodhost.com/forum/dedicat...s-windows.html (Linux vs Windows)
Hope this helps