I know that all you've said is true, and I agree with it. Open software is a blessing, built by generous people. If other people want certain features, they are welcome to contribute patches. I want you to know that I agree with this, I've never disagreed with that.
I'm arguing on behalf of a simple hypothesis, that Windows users know Windows and do not know Linux/Unix or POSIX. Moreover, they may not want or may not have the time to learn Linux/Unix or POSIX subsystem. They do not know nor can take advantage of what a "free Unix-like environment" provides. They know what they know. Cygwin adds a heavy emulation layer into Windows which they do not know. To be clear, they do know JavaScript and they do understand what running JavaScript on the server means.
Is Cygwin a technological achievement in and of itself? Yes, absolutely. Is Wine? Yes, absolutely. Is ability to run node.js or git on Windows through Cygwin? Yes, absolutely. Is that an awesome hack (in the best sense of the word) for people that understand the Cygwin emulation layer? Yes, absolutely. Is it an achievement for Windows-only developers and users who don't understand -nix idioms or POSIX subsytem? No, it isn't.
That's all I'm saying. I'm not offering a better solution -- I don't have one. I'm just saying that when someone from the -nix side says that something runs on Cygwin that they should respect and empathize with what that means for Windows users operationally.
To use an analogy, earlier a youtube video was posted about a first encounter between a tribe in Papua New Guinea and some white travelers. The white people had amazing tools are artifacts -- mirrors, matches, plastic cups, knives, etc -- which the tribal peoples had never seen before nor had a framework of understanding within which to reason about them. Are the tools cool? Yes -- the knife whittled wood far more effectively than their crude tools. Are the tools scary and hard to understand? Yes -- the tribesman covered the mirror with a leaf (!) because he couldn't understand how it worked or if it was (presumably) some sort of magic. The *nix command-line/file-system/permissions apparatus is incomprehensible magic voodoo to someone who's only had Windows console experience their entire life. So for the "white man" to say "but it runs in Cygwin" to the primitive native peoples is perhaps a tad presumptive. That's not to say that the native peoples are lesser beings intellectually viz. "don't eat that poisonous flower", Windows has had IOCP since NT4.
I think it's a wonderful example of the way the process should work that Microsoft is stepping up to help Ryan/Joyent port node.js to idiomatic Windows.