High speed rail is nothing like flying or driving. It's a lot faster on many routes for a start. No going to the airport and going through security, waiting to take off and disembark etc. Much faster and more direct than driving, no traffic jams. It's a lot more comfortable, you can relax, work, eat or whatever.
Places that are a long way away are suddenly just a short train journey away. It's fantastic for visiting places, fantastic for business. Japan's economy benefits hugely from having high speed rail, even if the cost is high. Japanese companies are willing to look at the long term for ROI.