I think it's better, "Czy nie jesteś mężczyzną?" is more like "Aren't you a man?" as if you still hoped that the answer will be "I am a man."
The reason I ask, is because (correct me if I'm wrong) it looks like it uses the feminine endings for the accusative case. It looks obvious to me from other lessons and pretty much everything i've been doing so far that mężczyzna is a masculine noun, but is this example with the feminine accusative ending just one that makes the word irregular?
Well, it's a masculine noun that looks like a feminine one and undergoes declension as if it was feminine. But it's definitely masculine and takes masculine adjectives (wysoki mężczyzna).
There are more masculine nouns ending with -a.