As for deployment, if your .NET app doesn't have highly specialised dependencies you're likely to get away with a simple file copy deployment. Even if you do need to install some frameworks/packages, offerings from e.g. ScaleXtreme (who allow you to manage both Windows and Linux servers from a single dashboard, private or in the cloud), make managing instances (via templates, scripts and integrated monitoring and patching) extremely simple.
This is great because I prefer writing my code in C# and running it under Windows but prefer Linux for the heavy-lifting (PostgreSQL, memcached, nginx for static content, etc.). I do accept that not everybody knows how to use both platforms or would like to learn, however that is a matter of preference not practicality. I'd say the two platforms are on par with practicality.
[1] https://aws.amazon.com/amis/microsoft-windows-server-2008-r2...
Firing up a linux instance does require more sysadmin skills from the command line (this can be non programmer skills to some), compared to a gui based OS.
Disclaimer: I use linux myself but have spent enough years in the professional world to know that there are things that windows can do equally well, just don't ask it to do everything. A basic startup stack of IIS (included), mysql, and a framework (download asp.net MVC) doesn't take much setup.
As for the sysadmin on the software side, I agree most .NET devs that want to build something probably have those skills. It's the hardware aspect that I think needed to be addressed.
The OP espoused the easy scalability of .NET using the Stackoverflow example without mentioning that they colocated with dedicated hardware.
SQL Server's a little harder to setup but it scales really well vertically (unsurprising given its Enterprise origins). As with most databases it really needs to be installed on physical hardware for the best performance.
Edit: Double-Jesus on a stick! I counted ~6 of YOUR references in this one thread. Pretty unimpressive.
Deployment's always had a variety of simple-to-complex options just like everything else.
As a former .NET guy, I think the hosting part of deploying .NET wasn't well addressed by this post.
Jeff Atwood built and colocated a dedicated 2 or 3U server to run Stack Overflow. I certainly wouldn't call that an easy or recommended thing to do for a startup, especially if none of the founders have enough hardware and system administration experience.
Compare this to signing up for EC2, Linode, or Rackspace and spinning up a Linux instance to run Rails, Django, or Node. Even easier to just spin something up for free on Heroku. These are mature, solid solutions being used by many startups today.
There are a few providers like AppHarbor that are trying to make .NET hosting a bit more startup friendly, but there weren't any mention of those in this post.