Let's review the situation. We have a quite high speed transportation system in modern aircraft. We choose not to disrupt cities by building them downtown. (And "we" choose all those security/time trade-offs.)

You suggest that we will tear up the hearts of LA and SF to build direct train-tubes, and then we'll let people breeze on board?

You can put a train station mostly underground, with only a relatively small area aboveground. An airport is going to be 4 square miles, completely above ground, an entirely different story.

Currently with the only "fast" train in the US, you don't need to get on early, or go through special security. Why would this be different?

Are those tubes bulkier than current train/metropolitans ? Even cities like Rome dig underground to build urban transport, even if in those cities hearts you can find more than just soil.

If it really is a "tube" it's a "big dig."

I thought the reason we don't build airports in the middle of our cities is that jet engines are quite noisy and could cause lot of property damage (not to mention discomfort) if operated next to other buildings.