The Matrix doesn’t have a single interpretation. I think pretending that The Matrix can only represent one thing and one thing only takes away the beauty of that movie. There’s so much going on that it’s possible to have completely different, yet still valid, takeaways.. There’s enough religious symbolism and nods to suggest its a story about spiritual enlightenment, for example.
However, one can’t deny that The Wachowski’s experiences as queer people played a big part in the the themes they were trying to express. Switch was originally supposed to be a different gender in The Matrix than in the real world, which would have been the most obvious evidence if the studio didn’t force that change. Also, one the sisters Has talked about how she nearly committed suicided by letting a train run her over. She mentions how she had so much shame about her identity but on the train tracks she had an awakening on who she was - she regained the will to live. The movie’s turning point is on the train tracks. It’s when Neo truly becomes the one. Agent Smith is holding him down and trying to let the subway run them over before Neo truly believes in himself and is the one. It’s where he truly adopts his new identity as Neo - he even corrects Agent Smith by saying “My name is Neo!” before becoming self-actualized.