I am no expert photographer, but allow me to give my two cents as well.
If you delve deep into the various photochemical processes used throughout the history of photography, or if you want to make your own film/paper and developers, you probably need to learn a lot of material. But very few people do this.
Then, there is the aesthetic aspect of creating photographs. This is largely a matter of taste, and again, one can read dozens of books without "understanding" it - probably because there is no objectively "correct" way to create a "good" picture.
The technical process of exposing the film/processing the picture data is, however, straightforward and easy to understand. It is just that there is a lot of mystique, rituals, and anecdotes about it that cause a lot of confusion.
The zone system is regarded by many as one of these rituals that make things look much more complicated than they are. And, as with other rituals, it often serves more of a social role (distinguishing zone system devotees from zone system heathen) than it has a scientifically sound foundation.

The "zones" that give the system its name are after all purely arbitrary classifications of shades of gray ... :dunno:
It is not that the zone system leads to bad results, it just puts unneccessary fluff between the photographer and the simple concept of adjusting exposure and gradation (gamma) to accommodate the contrast of a given scene onto the medium, be it silver-halide based film or a semiconductor based sensor.
In digital camera terms, this simply means adjusting exposure and contrast so as to achieve a (subjectively) "good" histogram. If you photograph in "raw" mode, the zone system is completely meaningless, as the response of the image sensor is fixed (with film-based photography, one would adjust the film development). In the end, it boils down to adjusting "levels" or "curves" in photoshop to your liking.
By obscuring this simple concept, the zone system actually makes it harder to understand what is going on. As Andreas Feininger put it in one of his photography textbooks, the zone system makes mountains out of mole hills.