There are a couple use cases:
1) applications where the OS is a commodity - abstraction layer to IO (disk, network). MS solution is their PAAS (which is expensive).
2) existing libraries/services that aren't available on Win32 where it is hard to justify another server license just for .NET - this factors in to where I work; some code can't be .NET as there is already a Linux server in the setup. We've ended up with 80% dotnet and 20% python
3) most companies loathe mixing server OSs; some shops have fallen into the MS camp and others the FOSS camp
4) The proof that they aren't going to cannibalize existing OS/SQL License sales is in your comment