As mentioned by others, the emphasis in the name is on the fact that it's a Windows Subsystem. The historical precedent for this name is "Windows Services for UNIX", which similarly provided a Unix environment on Windows NT.
THAT IS IT! I was wondering why the name always felt funky. Although the name they have now is technically correct if you ignore standard noun to adjective conventions.
I believe this, like many things in the windows ecosystem, is deliberately confusing/takes advantage of linguistic ambiguity to create confusion in the observer and create a sort of implied sense or feeling of microsoft superiority...
E.g. having windows 1st sort of inflates the 'primacy' of windows with respect to linux; it is linux that is being made compatible with windows rather than the other way around.
Best things that come to mind are things from the windows UI - like the network privacy zones, having the 'basic' and 'advanced' control panel, etc.. Some things say 'windows is updating your computer' rather than 'your computer is updating windows' or some such... To me they have this sort of psychological undertone of 'always remember how microsoft is helping you make this confusing thing much easier.. you couldn't do it without us'
That's not the entire story, unfortunately. There are other rules. For example, Windows might be considered a family name, as there are several Windows Operating Systems. Also, this is a technical name, and technical writing often follows different rules, specifically in cases such as this.
For the possessive form of Windows I would look at the Microsoft Manual of Style, which for me is the fourth edition.
Page 184: Possessive Nouns
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Do not use the possessive form of Microsoft. Do not use the possessive form of other company names unless you have no other choice. And do not use the possessive form of a product, service, or feature name. You can use these names as adjectives, or you can use an of construction instead.
Microsoft style:
the Windows interface
Microsoft products, services, and technologies
Word templates
> The correct form of possessive context for words ending in "s," is with a dangling, trailing apostrophe, and omission of the extra "s."
That is correct (or, at least, nearly universally agreed to) for possessives of plural nouns ending in “s”, style guides are mixed when it comes to other nouns ending in “s”, though the most common rule seems to be to use “’s”; while “windows” is plural, “Windows” as the name of the operating system is a proper noun that is not treated as plural.
I disagree. Microsoft is correct; mostly if not entirely.
Q: It's a subsystem? What kind of subsystem?
A: It's a Windows subsystem?
Q: A subsystem for what?
A: It's the Windows subsystem for Linux.
As another commentator mentioned, there's probably a missing possessive ("'s"), but even if we take the proper name to be more of an adjective modifying/qualifying "subsystem", it's a Windows subsystem, it's purpose is running Linux... the Windows Subsystem for Linux.
Now, we have a Microsoft system that runs the Linux binaries, which are GNU according to Stallman, but not running them on the Linux kernel. You’re naming the entire system after the one component that is missing. By the same logic that normal Linux should be GNU/Linux, Linux containers on Windows should be GNU/Windows.