There's no need to have only one line to connect everything, even in a linear structure. It's still about the topology.
At the simplest there would be one line connecting from end to end, which should be the fastest and the one with the fewest stops. But then you have smaller lines, travelling in their own tubes, connecting local areas. That way you can travel between any two points relatively fast and avoid congestion. You can build redundancy into this system. But also, it's not a catastrophe on a normally 20 minute trip if there is blocked section and you have to walk a few minutes, take a local connection to bypass the blockage and then go on. Happens to me all the time...
The big benefit in a linear city is that the transport pods never need to turn around. You also don't need to manufacture curved rails or things like that. You can build structures like that in a "2D" city, but it's harder.