Hi Victoria. Good question. Japan’s rail network is so good and so reliable, it’s hard not to go past it. But then the roads in Japan are equally as good.
If you’re moving around a lot and want to go to more remote parts of Japan, a car would be better. But if you’re going to be close to the train lines and your JR Pass covers the regions you want to visit, trains (and then maybe use buses, taxis or even short-term hire cars in between) would be better. Cost-wise, the rental rates in Japan are about the same as the JR Pass you’ve quoted here, but that’s for a compact and doesn’t include petrol or any insurance you might want to take out etc.
For me, the biggie is the JR Pass gives you access to some Shinkansen high-speed trains and their excellent ‘Joyful Trains’. Both must-do experiences.
Hope this helps. Let me know if you have more questions though – Jim