The immediate meaning is that the cow is like a "black box" A . That is... it is treated as a device -- a machine -- that gives milk, as long as it is given food etcetera.
However, a contextB is implied; it is not the machines that view the cow as merely a device that produces milk; it is human beings -- on one side, those who want milk, and, on the other side, those who make money from producing milk.
That is... the point of calling it "the cow in the middle" is about, not the immediate fact that it is in the middle, but that the persons [who want milk or money] do not care about the cow.
(This is obviously the point of the article containing the quote. The point here is that there would be available a more dignified/caring/respectful label for the cow, if the point was not that the cow is being ignored.)
A "Black box" [often shown with quotation marks [""] ] means a machine that just does something -- we do not know, or do not care, how.
B Here, context means, not sentence context, but real-world context.