It is quite rare, relatively speaking, to see websites running on MS tools. Its partly a historical thing - ie the "de facto" standard for webapps is a *nix system, and that means that most new webapps are written for *nix systems. That's just the same as desktop apps are written for Windows simply because the majority of desktops are Windows.
Apart from the history, where IIS was pretty poor, had a poor security record and was very much locked-in to Windows langauges (ie vbscript in ASP or ISAPI)(though you could run cgi apps), things have improved somewhat nowadays as languages like PHP have been ported to Windows with a lot of support.
Still, as the majority of websites still are *nix based, so not only will you find it a lot easier to obtain web skills from *nix people, you're also going to find a lot more information on working with the tools based on *nix systems.
Scalability. The TPC benchmarks always showed Windows systems scaling well... but you needed a f***lot of Windows servers to get the same benefits as a single Sun or IBM 'mainframe'. Those heady days where the 'one box' v 'one cluster' are over now - no-one really cares today, servers have become a lot more powerful so the differences are reduced. that said, the current top 10 TPC-C benchmarks all show *nix systems, and the TPC-H benchmarks show Microsoft systems doing well at the small end, but getting beaten into submission at the top-end tests.
However, one important factor there is cost of maintenance. More servers = more trouble = more time spent keeping them running. That can mean more expensive staff.
However, even SO is a minnow compared to, say, slashdot, and when you get a site with so many subscribers that your sitename becomes synonymous with a denial-of-service 'attack' you need to have some serious load balancing and architectural options. *nix systems have this, they're well known and widely supported (in fact, said systems can be used to load balance Windows systems too as they are delivered as standalone servers, running linux or a bsd OS), but that means you need *nix skills in order to get the most out of them - which, if you've only got Windows skills, you're going to have to do some learning. You might as well save yourself time and just learn the 1 OS!
Licencing: MS is getting better at giving away cheap OS for the web, Windows Server Web edition is a lot cheaper than normal Windows, but if you're running a large scale site.. you're going to want to upgrade it to Enterprise or even Datacentre edition, and those babies are not cheap by any means. And you'll want several instances running. And if, you're entirely Microsoft here, no doubt you'll be using other MS products, Office tools like Sharepoint or Biztalk or Commerce Server or SQL Server or whatnot. And those are not cheap either.
Compare that with the *nix solutions, you can guarantee they're free. OK, you may run Oracle DBs, but even so, that's cheaper than the whole MS stack. it may not matter so much in the big scheme of things, but if you're a small startup with a choice, free trumps any price. If you're a huge slashdot type site, free trumps hugely expensive.
Ultimately though, the free tools are rather good - good enough that all those sites use them. MS may produce lots of cool toys, but they're more like the Java of the MS world, and if you're going to run memory-hungry apps, you might as well use Java anyway. If you want to just get on with creation of a site, python or perl or php or ruby are all available to you on the free systems.