Previously the difference between Linux and Windows hosting made a huge difference. Picking which operating system to host your website made a huge difference in what you could do with the server and what you could accomplish with the website. However, in today’s context of cross-system web hosting, there is little that practically separates these two operating systems: Linux and Windows.
The first unique difference is how you access the server. Generally, both offer FTP access to your files, however, Linux is the only one that offers telnet or ssh access. This is probably due to the target audience that each operating system targets. While windows is targeted to the mass public, linux is probably more focused in that it provides many more features that would only be demanded by programmers and people familiar with computing and programming. In any case, while this may seem like a fundamental difference, there really is very little to separate FTP from telnet or ssh in the practical sense. While FTP allows you to download the file to work locally, telnet and ssh allows you to modify the root file on the web server by using unix commands.
The second difference between linux and windows hosting is that windows and linux support different languages. Linux tends to be associated with PHP, Perl and CGI while Windows is usually associated with ColdFusion and ASP. The database languages are also usually different, with Windows favoring Access while Linux users use MySQL. Windows also writes its pages in .htm format while Linux writes its web pages in .html. Ultimately these differences are minor, but can make significant difference if you are not prepared for it. Trying to modify Access files while you are using a computer that only has Linux can often be a surprising exercise in futility for the beginning programmer.
In terms of security, people tend to argue against Windows, citing a whole host of vulnerabilities. This is correct in a sense; while Linux tends to have the same amount of vulnerabilities, it is patched and updated faster due to its open source and free nature. This is in stark contrast to Windows vulnerabilities which are usually patched every time a new service pack is released. However, security also depends largely on your network administrator. With good administrators, your website is safe regardless of OS.
Ultimately, the choice is yours to make, whether you prefer windows or Linux. It is better to pick a web host based on its features and service rather than on what operating system it is running on its web servers. As the difference between the two is very little. However, if your website particularly requires a certain language due to the programmers you work with or any other language, it would be prudent to check for system compatibility before subscribing to a web host. If you do not require such specific details, you should simply sit back and let the web host handle these complicated technical details and focus on your website itself. After all, the content is way more important than the programming language or the OS of the web servers.