Prototype, alpha, and core are different things.
Sure, build your prototype in whatever you want, that's quick. A prototype "should" be just that, and in a perfect world you'd throw it away and take the learnings to build your real implementation - now that might be your alpha or your core. Obviously, this doesn't usually happen, but it's an important distinction when thinking about things that will have a large effect on the the business.
Then implementing the product that you want to sell has a different set of issues.
Microsoft stuff is definitely easier to get into some corporate IT environments, for sure. Much of this really depends on the specifics of the product you're building.
However, as a startup, there are some major downsides to choosing that stack.
First, is that things (VS, SQL, etc) tend to cost money, even with BizSpark there is a cost of time if not money.
Second, is that choosing these technologies typically limit your flexibility with other parts of the business: it makes it harder to run on linux-based cloud providers, today's toolsets (GIT, Chef, etc) weren't designed primarily with Windows in mind, MS products are often designed for enterprise usage rather than broad scale.
But the real issue here, I think, is hiring. The pool of .NET Developers is getting smaller all the time, and engineers that label themselves as .NET Developers often have a different skills profile than what is optimal for a startup. If you want full-stack, cutting-edge, 10x developers willing to work for small pay and big dreams, those folks tend to be using a very different toolset. Are there great .NET devs out there that you'd want to hire? Absolutely, they're just a lot harder to find.