It costs a bit to get to/from the airport too, whereas with shinkansen you have all-you-can-ride JR within the city you arrive at, until you exit the final gate. I'd say there comparable in price.
It depends where you are. In areas not well served by the JR you can end up spending quite a bit on the Metro. But you're right the costs are comparable.
However given that, I think convenience is the deciding factor in the Shinkansen's favor.
However given that, I think convenience is the deciding factor in the Shinkansen's favor.