I think the intuition gap comes from the misleading arts education about colour. It's still common to teach in schools that primary colors for paint are blue, red and yellow - when the correct primary colors are cyan, magenta and yellow as everybody familiar with CMYK printing can tell. If you search the internet about mixing paints, almost every site claims that the primary colours are blue, red and yellow... So I don't think it's the subtractive mixing itself, but subtractive mixing with CMY colors (and not the wrong model of red, blue and yellow they are used to).

There's long history of arts education with this misconception, partly because suitable pigments for CMY colour model are relatively new invention. Blue, red and yellow also kind of work well enough, especially if you tweak the palette by having two shades of each as your "primary colors". (E.g. you can mix saturated green from cadmium yellow and prussian blue, but if you mix chrome yellow and ultramarine blue, the green will be muddy). It's kind of like instead of having a full triangular gamut of CMY space, you crop the corners off of the triangle and have a a sort of hexagonal gamut.

As primary colors are by definition "colors that can't be mixed from other colors", it's strange that in arts education they still claim that red and blue are primary colors, when it's obvious that red can be mixed from magenta and yellow, and blue can be mixed from cyan and magenta, as every colour printer is doing it like this.