The problem is vision: namely nobody has any. The folks who built NYC at the turn of the century had vision. They didn't just put in subway lines, they put in mostly four-track subway lines with room for express trains. They didn't just build commuter rail, they built a vast system (again with a lot of four-track to accommodate express trains) with stations in numerous little Westchester and Long Island town. Oh, and it was electrified in 1903 (kudos to Tesla, but all-electric commuting is very turn of the 20th century stuff).
Over 100 years later, we're still using that infrastructure. Today, of the 1.6 million people that enter Manhattan every day for work, 80% ride either commuter rail or the subway. This is a movement of people that would absolutely crush any other city despite their extensive highway networks, but New York handles it very well using ancient infrastructure.
http://en.wikipedia.org/wiki/History_of_the_New_York_City_Su...