You shouldn’t compare apples and oranges because they are both great but for different reasons and purposes. It isn’t anti-intellectual to recognize that apples are way better for pies than oranges are but if you want some amazing juice and don’t want to go through a whole process to make it good; oranges are the way to go.

This and the many other examples I didn’t want to fill this page with are the reason why it’s a saying. It’s much faster than prefacing what exactly said apples and oranges are going to be used for before giving a real answer and I personally feel it shouldn’t at all be taken literally.