Referring you back to this answer, the thing you need to understand about the world of the matrix is that it's a setup, a scam, a flim-flam. Everything you see inside the Matrix has been 'rebooted' dozens, if not hundreds of times before. The machines appear to have total control of the whole environment including the memories of its inhabitants.
The only people who aren't subject to this memory alteration are those who're disconnected from the Matrix and we learn, later that their entire existence is also a put-up job, a concoction, a hustle, a subterfuge. Zion is periodically destroyed and recreated by the machines to their own specification. This includes the knowledge they're given access to and the technology they're permitted to use.
It's arguable that the reason why Trinity is such a good hacker is that because at the start of each new loop, she's already got knowledge of advanced programming languages but there's no real evidence of this in the film.