No, it shouldn't, and I take it by this statement you don't live in NYC. I do, and have lived in Tokyo and other cities with excellent mass transit. While Tokyo's system is much, much better, it's pretty fantastic that I know I can always get a train home no matter what time it is, no matter where in the city I am, much faster than any ground vehicle would take me.
Everywhere else just runs replacement buses at night and it's fine. Yeah ok it's a little slower, but it means you're not running a huge train for five people.
There are way more than five people per train at any time of the day or night. Besides all the people with night and early-morning jobs, there's also the fact that bars are open until 4 AM. They call New York "The City That Never Sleeps" for a reason.
Even though trains are scheduled through the night, they shut lines down pretty frequently during overnight and weekend hours and replace them with bus service.
It always seemed strange to me that Philly is the only city I've been to that fully replaces the subway at night with buses.