Tunneling in the US is massively expensive, which is a huge problem for infrastructure projects. There have been some previous posts on exactly this topic ("why do projects in the US cost so much?").

And we are out of money / unwilling to pay for such projects. Australia is still relatively swimming in its natural resource boom and has funds to do that. And political willingness to invest in public transportation that's clean and efficient.

In California, public transport seems to be relegated to the status of a homeless mobility system / shelter, that most people reluctantly take and have to wonder why it's so badly operated. I don't think the idea will get far to tunnel under the rest of the peninsula. We can't even sort out the remaining 1 mile of Caltrain that was planned to connect to downtown SF and the Transbay center.

Aside from that, I believe there's a groundwater level problem under most of the places where such a line would go? I'm not an expert on that though.