1) As others have mentioned, .NET has a legacy of being expensive and closed, even if that isn't really true anymore.

2) .NET isn't really taught in college classes, and a lot of startup devs come more or less right out of college, using whatever stuff they learned as a basis.

3) .NET isn't sexy in a cultural sense. It doesn't have a shiny new flavor of the week framework, compiler, library, or whatever for everyone to trot out every 6 months and brag about on their resume.

4) .NET has the perception of being a "big business" framework, rather than something you use to bang out a scrappy MVP. Scrappy MVP is where a lot of startups... start, so the impetus is to use whatever tool flavor of the day will get you to customer #1 the fastest.