I would characterize the ostensible preference for Windows outside of academia as mainly inertia.
In corporate environments, the choice of OS is often dictated by application compatibility. If you have a corporate intranet which was designed to only work on Internet Explorer, you are stuck on Windows for practical reasons -- replacing it would be an expensive undertaking and bring little value, so you just live with the consequences of that previous decision.
Of course, that's just an example -- more common is probably the use of an array of enterprise applications which were designed for Windows, or work better on Windows.
Add to this the cost of hardware and compatibility concerns. From a cost-of-ownership perspective, the availability of commodity hardware with supported drivers is still a strong selling point for Windows, coupled with the fact that this is what you can expect current and future employees to be comfortable with.
Microsoft has some propaganda which attempts to argue that the TCO (Total Cost of Ownership) is favorable on Windows, but I find these claims dubious at best; and certainly, if you factor in user satisfaction, many users who have a say in how their hardware budget is spent definitely swing the other way.
Ultimately, for many users, the deciding factor is whether they need strict Office compatibility or not in their day-to-day work. If your organization heavily uses one or more of the Microsoft so-called productivity apps, the free offerings are often unacceptable, even if they nominally manage to open and save files in these formats.
Where these popular applications are not crucial, it seems that you can be more productive if you can avoid them.
In academia, then, central use cases outside of proper research are article composition and review (where typically popular word processors are less than ideal, and some disciplines heavily favor e.g. TeX), email, and web-oriented activities, where fortunately free and open source offerings are generally roughly on par with commercial alternatives. Whether you then prefer (or can afford) Mac or Linux is down to personal preference and budget.
Finally, of course, you might have an important research application which happens to be primarily targeted for Linux platforms (or occasionally, as the case may be, Mac, though this is probably no longer very common).