No, because trains are open-air, i.e., not in a vacuum, which is required to produce the pneumatic tube effect. That leads us back to orlanz's response, where we decide that above-ground pneumatic tubes are undesirable. I would offer that they're undesirable not only because they're unsightly but also because they take up space and will cause other kinds of pollution (light, sound, air, etc). Not to mention logistics of terrorism prevention... it's far better that a bomb on the Hyperloop go off underground than above (not that we want it to go off at all).
I agree with your other points though. Remember that we got here because Edison's electric company replaced Rockefeller's kerosene lamps, and Ford's automobile started to replace Rockefeller's trains. At the time there was a plan to connect all of America via passenger trolleys; you could ride from LA to NY, even though it would take you a couple weeks or so. So Rockefeller got Ford to replace his clean burning ethanol fuel with Rockefeller's own kerosene waste product: gasoline, and the nationwide trolley system was scrapped in favor of a highway system for cars. Now we're coming full circle with an electric powered train that can take passengers from LA to NY, in minutes not days.
The tunnel is hardly nonsense. Apart from passenger trains, it will become an effective way to move shipping containers and other large items quickly. Currently, shipping goods to and from Hawaii on those Matson freighters takes a month each way. We could also reduce the number of trucks on the road by shipping their contents via pneumatic tube.
There aren't a lot of trains in action because of several reasons. Not all goods that need to be shipped, or people waiting to receive them, can wait the duration of a cross-country train trip. Trains also need a lot more buffering to manage traffic, as they need more time/space to speed up and slow down. The system simply can't accommodate the level of traffic that an invention like the Hyperloop would fill.