(author here) I totally agree, we shouldn't be trying to bring down the perception of the species! It's just useful to be mindful/remember sometimes that we are still animals, which means we're still going to be predisposed to want to do stupid irrational animal things. Understanding the source of those instincts can help in bridling them.
Rather than saying man is a "naked ape" I'd say a human is an animal with a language facility.
The point here is not to bring down the perception of our species but to raise it for animals.