The Matrix is a complex film with many layers of meaning, and it is up to each individual viewer to decide what the film means to them. Some viewers may see the film as a trans allegory, while others may see it as a story about the nature of reality, or about the power of choice. There is no right or wrong answer, and the film can be interpreted in many different ways.

That said, it is worth noting that the Wachowski sisters, who directed and wrote the film, have both come out as transgender. In 2012, Lilly Wachowski said that the Matrix films were "all about the desire for transformation, but it was all coming from a closeted point of view." This suggests that the trans allegory interpretation of the film is at least somewhat valid.

Ultimately, whether or not the Matrix is about transgenders is up to the individual viewer to decide. There is no right or wrong answer, and the film can be interpreted in many different ways.
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