Both operating systems have their ups and downs, one of the main reasons that Linux is so raved about in the web hosting industry is the fact that the software is open source. This gives you a lot more control over the way the operating system and the software you are using functions. IIS may be a great web serving software, in the end however Windows in its entirety is more resource intensive than a core linux distribution. Linux allows you to cut out all the bloatware (including the desktop environment) for more operating capacity.
Another huge thing is cost, as a Microsoft Partner & SPLA member I understand that Windows is priced specifically for Enterprisee use, and thus this can be an inconvenience for a lot of people (operating cost to revenue ratio), whereas Linux is free in most cases.
Another is Control Panels, when it comes to hosting websites the most widely adapted control panel happens to be cPanel/WHM. I know some years back cPanel attempted to enter the Windows market by developing Enkompass, and though the software was great, the heavy restrictions set forth in Windows prevented them from providing customers with the functionality that cPanel customers have all grown to love. Plesk, though also popular, still lacks a huge amount of features that are looked at by customers as well.
Next off is web-software compatibility. A lot of open source software is developed to utilize technologies that are mainly powered by Linux based servers. This can cause conflict from time to time.
It all boils down to personal preference.