John jest moim bratem - John is my brother
John jest z moim bratem - John is with my brother
You always use instrumental after "jest", "jestem", "jesteście", "jesteśmy", "jesteś" (+ adjective) + noun. (But not "jesteś w", "jesteś na" etc.)
If you want to say "You are pretty", you say "Jesteś ładny/a" 'cause it's verb + adjective. It's a nominative.
BUT "You are a pretty girl" is "Jesteś ładną dziewczyn(k)ą". Verb + adjective + noun. It's an instrumental case.
In the same lesson, "a person is eating meat" is accepted for "człowiek je mięso". In that context, człowiek is just a generic version of mężczyzna, kobieta, or dziecko.
With "ona jest człowiekiem", we might be making an assertion about the dignities and rights members of society accord each other. True, to a large extent "person" in English works too, e.g. "Don't make her crawl on the ground. She is a person!" But "She is a human being" would give even greater emphasis in this respect.
It has been discussed here already:
We accept "person" in most sentences, like let's say "She is a nice person", but not in such a sentence that is more about the biological species.
Basically, any sentient aliens or other races in fantasy would be considered "persons" as well but not human.