Why do academics prefer Mac/Linux?

It's not entirely accurate to state that Windows 'dominates' in the commercial world. While this is generally accurate in Desktop and Laptop computers, keep in mind that the vast majority of web (and other) servers are Linux-based. Keep in mind that 100% of the TOP500, a list of the 500 most powerful computer systems in the world, are on Linux. Keep in mind that Linux, especially if you include Android, is almost definitely the most prevalent operating system (kernel) in the world in terms of number of devices.

A lot of academic institutions, especially in more computing-related fields, are big supports of open-source/FLOSS communities, and Linux is obviously a very big underlying part of such communities.

And, most key in my experience, for academic/scientific environments, Mac and Linux have enormous computational advantages over Windows - the underlying Unix architecture model and the inherent support of very useful shells like bash, very useful device handles (eg. /dev/random, or device IO handles), etc. These things make the development of custom code, especially for scientific, computational, or instrument-interactive purposes, a lot easier than on Windows.

Even if you're not using custom code, I'd venture to guess that absolutely any computing cluster worth its salt is being run on some kind of Linux. If you want to just use that cluster, it's far less hassle to SSH in with a Mac or Linux computer with SSH built-in, than having to use something like Putty and fiddle around on Windows.

In all, science is very heavily dependent on computing. And high-level computing is very dependent on Linux. In my view this is the biggest reason that very compatible Unix-like systems like Mac and Linux are far more prevalent.

It's not just Linux and macOS, it's UNIX (and derivatives) in general. There are a lot of reasons, but a few things worth noting that might not have been covered yet:

• BSD (incl. the BSD Sockets API), was originally developed at University of California, Berkeley. BSD subsystems are utilized by macOS, Darwin, FreeBSD, OpenBSD, et al.
• GNU (typically utilized by most Linux systems) is also heavily rooted in academia. Founder Richard Stallman has something like 20 honorary doctorates and professorships.
• Mach (utilized by macOS, iOS, XNU, Darwin, GNU Mach, Hurd, et al.) was originally developed at Carnegie Mellon University.
• Non-proprietary, free and open-source systems, software, projects, etc. (like Linux) aren't funded by high volume sales (like Microsoft Windows), so their development largely depends on contributions of knowledge and labour from postgrad research teams, and the academic & intellectual communities at large.
• These kinds of operating systems are particularly well suited for distributed & parallel computing, supercomputing, rapid development, prototyping, experimentation, computer science, and science & engineering in general. When people accustomed to well-funded, proprietary products like macOS and Windows10 (i.e. most people) try a Linux distribution for the first time, often their first impression is that it's ugly, unpolished, even "un-finished" or incomplete — like it's still in development.

And they're not wrong. It's constantly being developed, and kind of open-ended; you can add or remove anything you don't need or want. You can adapt it to your needs or to suit any specific purpose, and you're not stuck managing a giant, stubborn monolith that forces you to adapt to it, instead of the other way around. It's kind of like leasing a mansion vs owning & living in a workshop; they're suited to different purposes.
Academics often choose macOS when they're looking for a bit of a compromise between the dichotomy. It's nice and clean, and simple, and easy, and uniform, and respectable, so you can bring your mom or your girlfriend or your grandma, but you can peel back the shiny stuff anytime you want to get back to work in that familiar UNIX-style environment.

Windows reboots itself without permission. This is very inconvenient if your computer is doing something at the time. Mac/Linux do not have this problem, so they are preferred.

Some specialised hardware only comes with Windows drivers. Hence Windows is required. Occasionaly hardware requires a different operating system.

In practice I use all three.