* Will you be able to recruit top talent? In Seattle, not likely a problem. In the Bay Area, it's harder[2].
* Does the licensing cost make sense for your business? BizSpark is awesome, but it's not forever. In most cases the answer is yes, but not always[3].
* Are you willing to learn Linux too? You're going to run across something cool you want to use that only works on Linux, or works best on Linux. Redis, MongoDB, RabbitMQ, etc. come to mind.
I've built a startup on .Net before, and may do it again. The documentation for the whole Windows/.Net/SQL Server stack is amazing, and they're very predictable. With little effort you can learn enough to know how they'll perform, where they'll fall down next, and the next steps to move forward[4].
[1] I co-founded and was CTO of Loopt. We may have had product problems, but the tech never held us back.
[2] It's hard to find really good people willing to work on .Net in The Valley. They know their next gig will likely be at another startup, Facebook, or Google - .Net won't likely help you there.
[3] After BizSpark is over, look into SPLA licensing. It allows you to pay monthly for only what you use, and allows you to always be running the latest version. During all of Loopt Microsoft Licensing never cost more per month than an engineer, and the software saved us at least as much time and money. Remember, each time "The New Hotness" breaks, the time you spend debugging or migrating to something else is time you're not spending on your product.
[4] For example, Windows and SQL Server have great performance reporting. You'll know you need to get more RAM in a month, or switch to SSDs soon, long before you actually have problems.