The technology's only really been perfected in the last 10 or 20 years, well below the normal replacement cycle for this kind of heavy infrastructure. Give it time - it's inevitable.

Because railway lines, in the past, were not designed with autonomous operation in mind. It’s really only suitable for completely isolated systems (high speed bullet-train style lines walled off from their surroundings, or Western Australian iron ore trains miles away from anyone) or lightweight metro/subway style trains (e.g. DLR, airport “air trains”) that travel at low speeds or can stop quickly.

Upgrading is hard, retrofitting is harder (e.g. NYC subway runs on a century-old technology), and most importantly, it all comes with a hefty price tag, all for an incremental improvement only. Follow the money.