As someone who has done both Enterprise .NET and startup work, I have to say that the reason we didn't use .NET is much the same as the reason you don't rent a 2-ton backhoe to dig up a flower bed: cost and overkill. Yes, the backhoe might dig the flower bed faster, but it costs $5,000.00 to rent, there's a one-week minimum rental, and its treads tear up your yard to get to the flower bed. On the other hand the shove…
The only thing you really need to pay for is the actual Windows 2000-whatever servers with IIS, everything else you can get for free. Visual Studio Express Edition is free, the .Net framework is free, and you can integrate with all sorts of popular open source products such as MySQL, Postgres, memcached, Cassandra, etc.
I have yet to hear anyone using LINQ on anything that's not SQL Server, and considering the NIH syndrome in Microsoft, I wouldn't recommend it.