Energy has a cost. That cost is built into the price of the things built with the energy. Unless you think the battery manufacturers are giving away their product, the real cost of energy to build and transport the batteries is built into their cost, and therefore built into the cost of the car.
The car could well be selling for less than the cost to build it, but not by more than $5000 or so. Toyota denies it.
There are not that many batteries, and they are standard nimh batteries, not unlike the millions being used to power all sorts of things these days. The battery in the Prius is essentially a pack of "D" cell batteries. There are 168 batteries in the pack.
You can buy the pack of batteries on e-bay for about $1400.
In the modern world, the cost of energy is pretty well reflected in the price of goods and services.
Now, the cost of POLLUTION is not captured in the cost of goods and services. If we did, we could largely solve our pollution problems through the free market. And it would be a good conservative principle for each person to pay the cost of the pollution generated to provide them the goods and services they use.
You are right. To the extent that costs are internalized, we should all just buy the car that best suits our needs and financial considerations (i.e., what we'd want to buy without any enviro-guilt). It is possible that energy has some real costs not internalized (e.g., much of our military budget, to keep the Mideast from falling into jihadist or Russian or Chinese hands), and perhaps these should be addressed with import or pollution taxes, but it is implausible that the "real" cost of energy is even twice its nominal cost.