As moral agents that understand the impacts of letting species go extinct due to human activity ruining native habitats and transplanting invasive species, we need to weigh the odds of reducing their freedom for the sake of conserving the population. Think how the California Condor was revived after being declared extinct in the wild in the late 1980s.

What ends up happening with zoos however is that capitalism sinks it's claws in and influences these zoos to prefer profit over the well being of the animals, even going so far as to ignore scientist/veterinarian advice in favor of their trainers.

So long as it remains profitable to restrict the freedoms of animals (and humans), it will happen. At least until we do something about capitalism