Well there tend to be two classes of startups. There are the YC-like startups. Which I think are often college grads or recent college grads. College students are generally familiar with open source software. I certainly never touched MS software in college.
The other class of startups are those by relatively successful people who left their current job to start a company. More of the Spolsky model. Here you'll find a lot more MS-based stacks. Usually because they're familiar with it and with BizSpark the upfront cost is relatively cheap.
Of course these startups probably have different funding models, so you hear about them less on places like TechCrunch. Lastly, they are often more enterprise focused as their experience in industry has given them the ability to see gaps in the enterprise offerings (college students don't do enterprise focused startups) -- but they aren't exciting consumer technologies. But a companies like Topaz Bridge are still doing some interesting stuff.
People will (generally) use whatever tool they're familiar with, regardless of whether it is actually better for the job or not. Therefore it makes sense that the person's background will be a fairly large determining factor in what language they use. Someone (like me) that comes from a decade of developing "enterprise" .NET applications is most likely going to choose .NET. Someone with that same background is likely to be less concerned about the latest "cool" tech, and more interested in just getting the job done.
It also has a fair bit to do with resources. If you're running on little cash, it makes sense to use the cheapest tools and hosting available. Whilst, MS offer free version of all their tools, you still need to pay for hosting your app. That's the big turn off for many.
For us, it is a combination of my .NET experience, the fact that hosting price isn't a huge issue (our web design and .NET consultancy work covers our costs), and most importantly I DESPISE Linux with a passion. Queue here to flame me -->
The other class of startups are those by relatively successful people who left their current job to start a company. More of the Spolsky model. Here you'll find a lot more MS-based stacks. Usually because they're familiar with it and with BizSpark the upfront cost is relatively cheap.
Of course these startups probably have different funding models, so you hear about them less on places like TechCrunch. Lastly, they are often more enterprise focused as their experience in industry has given them the ability to see gaps in the enterprise offerings (college students don't do enterprise focused startups) -- but they aren't exciting consumer technologies. But a companies like Topaz Bridge are still doing some interesting stuff.