Taxes aren't really something that are up to the airline to decide whether to collect. What I don't understand is why BA and AA don't charge it and JAL does.

My understanding is that because there is no base fare, and there are no fuel surcharges (YQ), the taxes do not apply, because you don't charge tax on $0 fare. However, the "fees" still apply (September 11, APHIS fee, Customs fee, Immigration fee, etc). This is what AA does (and BA) and I tend to trust AA over JAL when it comes to appropriately calculating U.S. taxes.

I'm thinking of bringing this up to JAL but don't exactly know how to go about doing it. I fly this route a lot and the extra $40.10 every time will add up.