This is a case of under-investment and poor design. The London Underground, for example, the oldest underground railway in the world, manages 2-3 minute headways (29 trains per hour) on many central lines, both sub-surface and deep level.

Of course, you need to invest in the infrastructure to make it work, but it's very possible.

A quick Google suggests that in Tokyo they even hit 50 trains per hour, so one every 1m20s, which is insanely impressive.