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I imagine the hyperloop design where cars are independent makes drag costs worse compared to trains (compared at the same speed).

However, autopilot cars don't have to operate independently over long distances, in ways that specifically reduce air resistance!

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Presumably you mean they could follow one another very closely. If they're traveling at several hundred mph, that doesn't give following vehicles much time to react if there's a problem with a leading vehicle.

You basically have the same problem with high speed trains, or even ordinary trains. It's just that all of the "control" is entirely passive. If your drive and control systems can be made as reliable as the passive systems linking train cars, then that should meet the same level of safety. Also, have you been on the highway during rush hour? There's not that much buffer against a pileup, in a system much more prone to failure!

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