"Apex predator" doesn't mean "eats everything", but rather "eats what it please and has no predators of its own". By that standard, we're the most spectacularly successful predatory species this planet has yet seen, to the extent that many of us never have to hunt even once in our entire lives.
On the other hand, we're not actually eating all the species. Most of us are almost exclusively eating species that through the miracle of selective breeding have been bred to be delicious, nutritious and easy to kill.
We stopped trying to satisfy our dietary needs by way of becoming the apex predator once we figured out domestication.