There's nothing inherent in physics that prevents self-driving cars, but unless you want to jump out of a moving hyperloop pod, it has to come to a stop and accelerate again; and it does so slowly enough not to kill its passengers.
Just because you need to accelerate and decelerate doesn't mean you need to do it on the same shared track as the main line.
But that's not the whole story. If we have intermediate stations at all, we need to ensure all cars have the same speed when they get to share the same main tube. We need acceleration tubes the same way we need acceleration lanes in regular roads. (How to plug those tubes to the main one is left as an exercise to whoever builds this.) Anyway, those tubes need to be 25km long.
But that doesn't mean they have to be separated by that much. You could have a station every 5km if you're willing to run 5 acceleration lanes in parallel (and pay for them).
This gets even easier once you get close to the destination: even in the main tube, cars need to decelerate, starting at 25km from their destination. 10km away for instance, the speed is already down to a little over 300ms⁻¹. To join the lane at that point, you need only 10km to accelerate. Likewise, if you need to join 5km before the destination, you need to accelerate for 5km as well.
In other words, you could very well have stations as close as 5, 10, or 20km from the urban centre. You won't go very fast, but remember that at those speeds and accelerations, it's going to take less than 5 minutes anyway.
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If trains didn't have to stop at every station, and used acceleration and deceleration rail-roads where appropriate, their average speed would be much higher. First, they can't for 2 reasons: rail-roads are expensive and take land (so does an Hyperloop tube). Second, passengers need to go in and out. This means many stops for the same train. Hyperloop's uses individual, so it doesn't have that problem.
Untrained human beings can handle minutes of linear deceleration (perpendicular to the spine) at 12 g, and at least a second at 25 g. Strapped, mind you. And the limits are higher in backwards-facing seats (eyeballs-in is ~17 g untrained) with the additional advantage that very little strapping is needed.
Even that's a bit of an understatement.
> I picked 0.5g because that's close to what you get during an airliner take off.
You don't get any more than that even during landing?
For reference, I can easily decelerate harder than that in my car.
I'd say 1-2g over a span of a few min might be tolerable by the general population but might not be need to be researched for suitability for children, the elderly, and the disabled.
https://en.wikipedia.org/wiki/Slip_coach
Not sure if something like that would be practical in this instance, but never count out human ingenuity.
It remains to be seen how effective pumping can be, but as envisioned hyperloop is a point to point system. Switches are very difficult and must be done at low speed a) because of the slipstream disruption and b) because branching greatly increases the interior volume of an enclosed tubeset. It can be done.. but it's a level above the basic infrastructure.
Chicago's train system has 241 stations and carries 300k people a day. The furthest station is 62 miles from Chicago.[1] Takes more like 1hr 40 min. New York's train system has to be more more active.
1-Motorola was dumb enough to build a campus out there and then never used it.