N.Y.C. itself is another of their rules: put the dots in anything that seems like it might be an acronym or initialism, even when when the rest of the world stopped using the dots decades ago. When was the last time you saw NYC spelled as N.Y.C. anywhere, except for the N.Y.C. media?
These organizations will always write I.B.M., F.B.I., C.I.A., H.P., and so forth, even when those companies and organizations themselves do not use the dots in their official names.
What I can't answer, though, is your question: why do they insist on this even when it contradicts the correct usage?
Now in some fields, like computer documentation, there's practical reason to change. It would be confusing to capitalise command-names if they are lower-case in their (case sensitive) native language. But newspapers aren't bound by that consideration, and it doesn't really apply to company names anyway.
But that is still a rule that all proper nouns are capitalised. It's also beside the point. No one is claiming that rules don't change, or even that they are sharply defined. I was claiming that it is presumptuous complain about other people when they follow the traditional rules.
But there ought to be another rule that takes priority over that one: when you use the name of a person or company, capitalize and spell it as they spell it. They are the ones who get to decide. It's not the prerogative of a third-party publisher or newswriter to override that.
It seems like a simple matter of humbleness and deference to whoever owns the name. It's eBay, not EBay, and IBM, not I.B.M.
What I don't understand is why a news organization would feel it's their business to override that - and why it's especially prevalent in the N.Y.C. media.
It is entertaining though! :-)
Once upon a time, the late musician Prince decided to change his name. Turns out that no, you don't always "get to decide" and even fans don't follow your every whim: Most ignored his choice and without much "humbleness and deference" started referring to him as TAFKAP—"The Artist Formerly Known As Prince."
[0] http://nymag.com/selectall/2016/04/princes-legendary-floppy-...