My department is only .NET due to dependencies to specific third-party manufacturing software that is .NET and we use their SDK for a lot of stuff. 95% of our apps run on Windows, 5% on Linux. The Linux part exists only because management heard about it and mandated to try it, not because it makes any sense - the third party software runs only on Windows, so even creating 2 dedicated servers with Linux (out of several dozens with Windows) in every plant is just a major pain in the back and a complication that does not pay out.

But if you don't have dependencies and limitations to Windows and you can go full swing with Linux, it's a matter of overall cost and productivity, use what is best for you.