For anyone (like me) who raised an eyebrow at the "trans fats are highly toxic" bit, wiki helpfully mentions some recent (2013) FDA guidance on the matter: http://en.wikipedia.org/wiki/Trans_fat
To me the word wiki refers either to the original wiki at c2.com[1] by Ward Cunningham or the kind of organically grown community around a user editable website.
Do not let the word wiki in its name and the content being provided by users through a wiki engine fool you, wikipedia is not a wiki (for a variety of reasons) but this is a common misconception.
Let's just say that if openstreetmap had been called wikistreetmap and used a wiki engine, it would still be "a map of the world, created by people like you and free to use under an open license." and not a wiki.
So yes using wiki as a shorthand to refer to wikipedia is not only confusing but also wrong.
-edit-
meatball[2] is a wiki, consumerium[3] is a wiki
everything2[4] is not a wiki[5] and everything2 not being wikipedia[6] doesn't make wikipedia a wiki.
Wikipedia is estimated to be the sixth most-visited web site in the world, and is the only site in the top that is commonly referred to by the word "wiki".
You are free to complain about or dislike that, and to want people to broaden their horizons if they think of it as the wiki or as the default thing that "wiki" refers to, but you are not free to claim that most people, when they say "wiki" as a shorthand for a site, actually mean some other site, or that some other site which could be called "wiki" is more likely to be meant.
It does cause confusion. I use multiple wikis that are not Wikipedia on a daily basis. When someone just says "wiki", my first thought is that the sentence is not grammatically correct; it is like saying "encyclopedia says" or "book says", it's not grammatical without an article or other qualifier of which one you are talking about. My next thought is that they are referring to the original wiki, http://c2.com/cgi/wiki.
I have seen this usage become increasingly common, but I try to discourage it when I see it, because it does cause confusion, and if it catches on, could cause even more when trying to discuss other wikis as people may assume that you are talking about other Wikipedia affiliated sites, not other instances of the general category of wikis.
I'm honestly surprised there are people on Hacker News who hadn't yet gotten the message about trans fats. Trans fats are really, really bad. Far worse than the saturated fats they're attempting to replace.
Calling "Wikipedia" simply "wiki" is like saying "book mentions..." when talking about what a specific book discusses.