I don't think they're talking about the time required to develop on the Microsoft stack. They're talking about the cost of:
- tools (Visual Studio, Resharper);
- operating systems (Windows Vista, Windows Server); and
- databases (SQL Server 2005/2008).
And yes you could use Mono + Linux but that's a feature-incomplete implementation (at this point) and presents greater risk than the Microsoft-certified solution. Plus MonoDevelop isn't as good as Visual Studio. I think Mono is still fairly limited as a production option.
Microsoft has a program for startups (called BizSpark) that can effectively eliminate those costs for startups (less than $1m annual revenue iirc) but get beyond that and it can get real expensive. Based on some of Jeff's comments I have to wonder if Stackoverflow is deliberately staying below this level (by only accepting a certain amount of ad placements) to avoid this. Note: he hasn't said that. That's just a question that occurred to me.
But compare that to say a PHP or Java development stack:
- Dev machine: Windows, Linux (free), Mac or whatever;
- MySQL (Free) running on Linux;
- Apache or nginx (both free);
- etc.
That being said, the concept of using really cheap boxes, while popular, isn't universally better. You'll use a lot more power that way (compared to higher spec servers). And higher spec severs will tend to work out cheaper in commercial licensing costs than buying software for lots of cheap boxes. So you have to be careful in comparing commercial vs non-commercial solutions.
Take a look at Scaling Up vs. Scaling Out: Hidden Costs.
I don't want to get into the issue of the cost of development because there are too many factors to make any unqualified statements. Like any other stack, there are probably things it's good at and things it could be better at.