From an embassy page instructing people how to make the flight arrangements to get out of Japan:

Do I have to pay for the flight?
U.S. citizens requesting evacuation will be asked to sign paperwork promising to reimburse the U.S. Government for flight costs at a later date. Exact flight costs are not yet available, but should be comparable to a one-way commercial flight from Japan to the safehaven location.

That is the standard message they put up every time they start doing flights, so you will have to pay to get to the safe haven city, where they will have to make their own arrangements to continue on from there. One suitcase (don't think they charge for it) and one carry on per person.