The the air moving in the same direction as the car is how air resistance is combated?
you could completely fill the tube with train...
but seriously, I was doing some thinking, and if you're going to build a tube, I can't see why you wouldn't evacuate the tube.
The tube walls need to be a little thicker to account for the air pressure, but it's really not that bad. I think a 6' diameter tunnel would need like 0.3" thick steel. The material for all of the steel for that to get from SF to LA would be around $1b, which is a rounding error on the $90b CA high speed rail project. and even if you didn't evacuate the tube, you'd still need some material.... The cost of evacuating the tube is also cheap.
(Personally, I think a 6' diameter tunnel is sufficient height. An automobile is way less than 6' tall, and folks don't complain about how uncomfortable they are. but even if you go to 10', the material cost is still only a couple billion).
If you're going to bother building a tube and dealing with all of the road crossing headaches involved in that, why would you try to move 1 atm air through the tube at 1000mph, or move a car through 1 atm at 1000mph? Either of those options is somewhat crazy compared to the cost of just reducing the air pressure inside the tube.
If you go full vacuum, you need some way to scrub CO2 out of the trains for the air breathing passengers, but at 0.1atm, you could probably just pull that air into the car, and you'd only have 10% of the losses you'd have at 1 atm.
If CA is going to put $90b into a rail project, it would be nice to get something out of the project other than a slower, more expensive way to get from SF to LA than via airplane
(more expensive if you remove government subsidies: if 10,000 people ride the train every day for 20 years, the cost per ride would be over $1k, even excluding operational&maintenance costs. If you assume that 100,000 people ride the train every day then the cost becomes more reasonable, but we currently don't have that many people riding planes between the cities, and planes are faster. 10,000 folks per day seems generous to me.)