In a recent interview with Lilly Wachowski, she spoke about the movie's true meaning, explaining that it was a metaphor for the trans experience. Fans suspected as much for a long time, but this is the first time Lilly or her sister has confirmed the theory on an open platform.

Audiences newly privy to the information are likely to assume Neo's transformation from Mr. Anderson to The One (Keanu Reeves) is where the Wachowski's focus was at, which makes sense. He goes through the entire first movie, learning to be who he was supposed to be, defying previous societal expectations of him. That, in turn, sounds like a metaphor for the experience many transgender individuals go through. Lilly, however, had her mind on another character.

 Switch (Belinda McClory) was supposed to change genders once inside the virtual world. The original script depicted Switch as a male while outside of the Matrix and then as a female within. Said detail would've made the trans metaphor much more transparent, of course, that's presumably why Warner Bros. nixed the idea when it was originally pitched to them.
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