Unfortunately, it is very expensive to operate that way. The easiest tunnels to build are the ones Paris did for their subway a century ago: dig up the soft limestone under the street, lay tracks, close it up. But you still need to deal with ventilation (especially for non-electric cars), fire suppressant, evacuation, flooding and general maintenance. In the best-case scenario, tunnels are just very expensive.
Then there are places like Atlanta (sitting on granite) or San Francisco (in a fault zone) where things get a lot more complicated.