What I like about a place like Tokyo is that you can choose the mode of transportation that is most suitable for your journey. If you're someone who likes cars, there's no shortage of roads and highways. It's a great way to travel into the mountains where the trains can't go.
Personally, I use my bike whenever possible, up to about a 30 minute journey. Farther than that, or when the weather is bad, I use the train. If I need to go somewhere remote, I can rent a car or call a taxi.
As for a commute, housing is cheaper here than you'd expect, partly because housing is not viewed as an investment. It's not difficult to live near where you work, if avoiding the trains is a priority for you.