It wasn't just that different things respond differently, it was that some things respond poorly and the beans respond well. But the metaphor only works if you accept the conclusions and don't try to examine it closer. For example, did either of the characters in the story taste the water? If the whole point is that the beans changed the character of the water, it does your metaphor a great disservice to ignore the fact that the carrots are going to change the flavor (admittedly it's not going to be as nice as the coffee, but it's the exact thing that the center of the parable hinges on).
As an example of what I think is a nicely constructed metaphor, look for the first metaphor in Book I of the Aeneid (too large to reproduce here, check out http://classics.mit.edu/Virgil/aeneid.1.i.html and search for "His finny coursers"). It comes in the scene where Poseidon is calming the seas of some rogue winds loosed by Aeolus, and compares him to a "grave and pious man" talking down a rioting crowd. The correspondence between the rioting crowd and the sea is intuitively clear, and the modern innovation of modeling crowd and traffic behavior with techniques from fluid dynamics serves to reinforce it. The image of calming the crowd with "sober words" lends insight into Poseidon's approach toward his domain. On a personal level it also invokes the story of Joshua Norton calming a San Francisco riot by reciting the Lord's Prayer in the street.
The point (which I've taken an awful long time to get to, I apologize) is that unclear and ambiguous metaphors tend in my experience to bely unclear thinking. When I can rewrite a story as I read it to have the opposite meaning as it was supposed to, it suggests to me that it was not written in the first place with a critical eye.