It is unlikely that the home user wishing to run their own website will have much concern over what system their web pages are going to be hosted on.  For most, the choice of selecting a hosting package will come down to cost, and what features and services are offered for the money.  The concentration should be on that and not the language.

This is fine, because the choice between the two operating systems is only divided by a thin gray line.  They both support access to files through FTP, and many the same file types can be used on both Linux and Windows servers.  CGI scripting and MySQL databases are also supported by both systems.

There are pro’s and con’s stacked up on both sides of the hosting scales.  Linux is open source, free and excels with MySQL and PHP, which are also free. Windows servers can cost to be set up, and they are invariably a little easier and user friendly to configure.  Both supply a good range of software ranging from free to expensive.

Whilst there appears to be no clear leader in the market, for the professional web developer, it may simply come down to a choice of what language you prefer to script in.  ASP and .NET environments are all unique to the Windows server, so if you are working with a web programmer who scripts in one preferable language, then the choice could be made for you. The programmer will invariably make the website, not the scripting language.

Security is always an issue, and Windows systems often take the brunt of attacks by people wanting to exploit weaknesses, just for the sake of doing so. You can follow all the security arrangements, but if someone is intent on hacking into your site, then the chances are, they probably will.  That fact alone raises the point that whilst they try, neither system offers 100% guaranteed security.