There still are a few differences. The first difference is how users interact with the server. Usually, both offer FTP access to the files. Yet, Linux is the only one that offers telnet or ssh access. More than likely, this feature is aimed specifically at their respective target audiences. While Windows is targeted to the mass public, Linux is more focused toward the features that programmers want.
Everything considered, not much separates FTP from telnet or ssh. FTP allows you to download and upload your files and with telnet and ssh you can alter the files using UNIX commands. Most people will never need to bother with this particular aspect of web design.
The second difference between Linux and Windows hosting is that they support different programming languages. Linux is usually associated with PHP, Perl, and CGI, while Windows is associated with ColdFusion and ASP. The database languages are also dissimilar, with Windows users favoring Access while Linux users prefer MySQL.
In addition, Windows also writes pages in .htm format and Linux writes its web pages in .html. Ultimately, these differences are small, but they can make significant difference if you prefer a particular language. Attempting to modify Access files while you are using a computer operating system based on Linux can be an exercise in frustration for beginning programmers.
Linux hosting plans differ from Windows hosting in other areas as well. As far as security, people tend to think that Windows is unstable, listing a whole bunch of vulnerabilities. For the most part, they are correct. Although Linux tends to have a number of vulnerabilities as well, Linux does a better job of updating and patching because they are open-source software. Windows vulnerabilities are patched every time a new service pack is released. For web design purposes, security mostly depends largely on the network administrator. Good administrators protect your website no matter OS it is on.
Ultimately, the choice is yours. Whether you personally prefer Windows or Linux, it is smarter to pick a Linux hosting plan or a Windows hosting plan based on the features and services it offers. Especially since the distinctions between the two are small. If your website needs a specific language for any reason, then it would be wise to check for compatibility issues before deciding on a web host.
If these things are unimportant, you should probably allow the administrators to determine if you need the best Linux hosting plan or whether you should use a different OS. Your energy should be expended building a good website with content that keeps visitors engaged. Do not worry waste valuable time trying to compare Linux hosting with others. Focus on the things about your site that matter and leave the debate about the operating system to others.