The phrase isn't wrong, though. The vast majority of FPSes involve you playing a man, shooting other men. Sometimes it'll include a woman, but only if she's very, very scantily clad.
I always thought of it as more of a fantasy/RPG issue.
(Similarly unrealistically proportioned male character with armor missing on stomach: http://img3.wikia.nocookie.net/__cb20120215221956/quake/imag...)
Which has nothing substantial to do with a "phallus" of any kind.