Wanna spin up n VMs for production / distributed computing? For Windows, you have to license each VM, whereas with Linux, the incremental cost of another node is nearly 0.
(Side note: I had high hopes for container support on Windows Server 2016 because unlike OS's, containers don't require individual licensing. Unfortunately Windows Containers are still immature, and are ironically second-class citizens in the Microsoft ecosystem compared to Linux containers)
Wanna spin up a n database servers? A single SQL Server (Enterprise) instance is pretty pricey (and it's licensed per core, minimum 4), whereas Postgres is free for any number of users and any number of processor cores. You want several replicas of your SQL Server? It is $$$. With MySQL, every replica is free license-wise (there are other costs of course).
The cloud has changed these calculations somewhat, but if your infrastructure is on-prem, Microsoft licensing can be prohibitive at scale.
In addition to costs themselves, Microsoft licensing is a highly complex topic. One of my colleagues who deals with Microsoft jokes that someone well versed with MS licensing deserves a PhD. A lot of people simply don’t want to deal with all that when they have a thousand other things to worry about.