The gorilla could represent a variety of images or ideas. Let's think of the purpose of the book. Dan Quinn wants to convey that humans cannot sustain themselves at their current rate of consumption. Humans take resources from the earth and leave waste at a rate that is unseen among any other living thing in the world. This is likely a cause of what today's population values. For example, in their process of consumption, Quin points out on pages 218- 227 of Ishmael, that humans today focus on accumulating knowledge on what works well for things (i.e., a factory, a car, etc.) while human tribes before the year 8500 BC would accumulate knowledge on what worked well for people. In other words, the former focuses on materials while the latter focuses on people.
Before our culture changed into what it is today, humans use to hunt and gather their food, changing locations as weather conditions and food supplies shifted. They were part of the earth, just as a fish is part of the sea or buffalo is part of the prairie. They lived in concert with the earth, taking only what was needed.
So how does all this relate to your question? The gorilla is not open and free and in the wild. He speaks to the protagonist only through a cage. The gorilla has been taken from his natural habitat in order to improve what works well for things (in this case, the thing is a zoo and later a circus). This caging leads to the gorilla's acute physical sickness. Nonetheless, throughout the story the gorilla is conveyed as a master teacher and as sage-like in his wisdom. Thus the gorilla symbolizes humans in their current state. Humans are a caged animal, no longer free to live as were intended. Consequently, we (or at least our habitat, the earth) are getting sick. So why didn't the protagonist simply speak with another insightful human throughout the story about the condition of ourselves and the environment? Probably because the gorilla is still a wild animal and, like all other wild animals, can speak from the perspective of a species that still lives with the earth.
Ishmael represents the strength of nature and how easily it can take back humanity. The glass he is sitting behind represents the fragility of the relationship between nature and humanity
the gorilla is ishmael a man in a gorilla body