They're safe, inexpensive, and run frequently. Vending machines sell tickets, and if you err and underpay for your ride, you can pay the difference at your destination. Some machines also have an English-language option that can be activated when buying tickets. While a fairly expensive way to travel, taxis are good for short trips. Remember that a red light means the taxi is available while a green light means the taxi is occupied.
Taxis are plentiful around well-known spots and major hotels.
On one trip, we actually had a driver through up his hands in disgust at his inability to locate a particular restaurant and kick us out of the cab. Transferring between subways and trains can be tricky. There are single-day economy tickets as well as passes that allow a day's travel on all the subway systems and busses. A valid JR Rail Pass allows unlimited travel on JR Rail Lines. They exist everywhere.