Although Windows dominates the Desktop operating system world, eclipsing Linux, Mac OSX and all others combined, that's not the case when it comes to web servers, with Linux being the most popular. There are pros and cons for both systems, and the choice depends on your specific requirements.
Firstly, what kind of development language or database are you planning to use? Universal languages such as HTML and CSS can be run from either Linux or Windows hosting systems, both can support MySQL databases, while Windows systems can only support Microsoft SQL (MSSQL), and generally the decision comes down to whether you’ll be using PHP or ASP to build your website.
Linux supports the most common languages and databases, including PHP, Perl, Python and CGI scripting, which are the standard for web pages that require podcasts, shopping carts, and blogging software such as WordPress.
Windows hosting is designed for users who will be using Microsoft’s ASP, ASP.NET, MSSQL or Access databases to backend their websites. It is possible to include such features as blogs and podcasts, and create a shopping cart, although ASP and ASP.NET applications typically require programming on your computer before they can be uploaded and used online. The operating system of your PC has little bearing on the web server software when building your site.
Linux web servers support almost all common proprietary software control panels, including Plesk, cPanel, DirectAdmin, H-Sphere, and Virtualmin Pro, while also supporting a myriad of open source control panels. Options for accessing Windows hosted control panels are fewer, with Plesk being the most common one, which offers only two open source options.
Linux is often considered to be safer than Windows from a security perspective, however, it depends more upon the server setup and the administrators running the server than the operating software itself. As long as the server is managed and maintained conscientiously, with the latest security and performance patches installed, as well as configured for optimal security by an expert, there is little difference between the two.
An important point to note is that Linux open source software, which enables it to be flexible and more customisable than a Windows web hosting system. This open source model also means that companies are not charged for using it on their servers, making it more cost effective. Hosting companies will pass on the cost of licensing Windows to the user, which will almost always makes it the more expensive option.