^D, Ctrl+D and C-d are all different ways of saying the same thing. There's nothing particularly neutral about Ctrl+D, any more than there is about using the word 'water' to mean the substance of which the oceans are mostly comprised — it's just another dialect's term.
The same argument you made could be used if the author used the unicode codes for Ctrl+D, which I find to be an indication that the argument was a bit weak. The article itself is written in English, and to expand upon your metaphor, tt would be strange to use the term agua to refer to water in an English article. Language is really based around what people use, so using what people know is generally considered good communication. If you use something different it's considered good form to explain why. Each representation you chose is effectively shorthand for the English phrase 'Control + D', just with different stylistic representations. People are much more familiar with Ctrl+D to refer to the key combination of Control and D.
Anyways, I had the same issue when I first started using Linux. It probably took me over a year to realize the caret stood for ctrl, and that's only because I accidentally typed it in something that printed the codes literally.
It's not about neutrality, it's about ease of understanding. For me at least, when speaking about something that can be entered into a keyboard ^D is less obvious than Ctrl+D–I need to press the key labeled "control" to issue the proper command, the key labeled "^" will not suffice.
To be really pedantic (sorry! I'm not complaining about your comment), your keyboard does not have any key labelled 'control', it is always (AFAIK) abbreviated as 'ctrl'. Which is really weird to me, as it's hardly a big word needing abbreviating, and keyboards often have other long words written on the keys ('delete', 'page down', and so on).
On top of that, the shortened 'ctrl' is really a terrible abbreviation. It's not obvious that it stands for 'control' and I would guess that most non-techy people would have no idea that it means this word. Plus, it's near to another key with multiple letters ('alt'). The overall effect is that 'ctrl' appears to just be a jumble of letters with some esoteric meaning. A really odd design decision. Why not just put 'control' on the key and be done with it?
You're incorrect, especially for the typical reader here. A good chunk (maybe not over 50%, but its gotta be close) of the regular readers on this site use Macs. Most Mac keyboards, including the ones on the Macbook Pro, spell it out. Same for most non IBM/IBM-PC compatible keyboards.
How odd! My mac keyboard is a similar design, but has 'ctrl', and has no writing on the shift keys, caps lock and so on. The only unabbreviated word it has is 'delete'.
Perhaps the standard is something to do with the country (mine is a UK layout).