I imagine because during their training of what the icon means, they will have been told about the reference. It's like how we all know the Rutherford model of the atom and what it represents, despite no human every actually seeing one in person... and it not being quite correct. Show someone an icon made from the Rutherford model and ask what it represents, and they'll say "an atom".
It's about training. Look at this picture[1]. If you made an icon from this simple structure, do you think people would understand what it meant? It's a pretty unknown bit of technology, but what it does has a clear analogue to a common function on websites. If only one site used it, it would be confusing. But if it were used by almost everyone, all through your growing up, you'd both understand the icon, and that it was shaped that way because it's meant to look like this object.
OK, I looked up what that thing is, and while it's pretty neat (and probably much less popular now so many people drink coffee) I'm not seeing the "clear analogue to a common function on websites". Can you tell me what website function you're thinking of?
Perhaps I should have said software rather than websites specifically, since websites tend to conflate both 'search' and 'filter' into the one function. They are pretty similar.
It's about training. Look at this picture[1]. If you made an icon from this simple structure, do you think people would understand what it meant? It's a pretty unknown bit of technology, but what it does has a clear analogue to a common function on websites. If only one site used it, it would be confusing. But if it were used by almost everyone, all through your growing up, you'd both understand the icon, and that it was shaped that way because it's meant to look like this object.
[1] http://www.reon-tuellensiebe.de/_EN/kategorien/Home/dateien/...