The zoo is the ultimate goal in this book, the place Ivan bends over backward to get himself and Ruby to in order to stop leading miserable lives at the mall. So while they're at the Big Top Mall and Video Arcade, the zoo represents freedom and a better life.
However, the zoo is also a place where captured animals live. And since this is true, it represents just how damaging captivity is to wild animals. Ruby and Ivan don't end up free in this book—they just end up in kinder, gentler captivity. And when they do, after decades alone at the mall, it's a process for Ivan to even acclimate to being around other gorillas, which makes it super clear that he couldn't hack it in the wild at this point. Captivity has stripped Ivan of his ability to make it on his own, and it takes guidance from humans to help him settle into life with his kin.
For a little more on the zoo, be sure to read up on television elsewhere in this section. Symbolically, the two kind of go hand in hand.