There's two issues aren't there?
1. Fashion and lack of awareness of .NET's benefits - php is more ubiquitous and probably always will be, ruby is more trendy. Don't underestimate the effect of programming fashion in startup culture. Some people would rather waste their time writing server-side code with immature tech like Node.JS than use something tried and tested like .NET or Java.
2. Fear of costs - People know they can always get Linux servers for next to nothing. I tend to think that if you're businesses sucess depends on eliminating the cost of a few Windows Server licences, then you've got a crappy business plan, but not everyone thinks like that.
I think a third point that goes beyond cost is simplicity. Startups don't necessarily start with expert developers. Lots are straight out of college. I am biased though since I work on this WebMatrix stuff.