I don't know if you'd call my company a startup as such, but we use the MS stack. However, the reason for that is because I knew it very well before starting the company. If I were a Java expert, I'd have used that, and so on.
Given that .NET Core is now pretty good, you don't have to worry about buying Windows licenses for your servers, and you can use VS Community so long as your company is small enough, so your startup costs aren't too bad.
In conclusion, it's been an excellent experience and I would recommend it, if you happen to know the MS stack well yourself.