Credit card issuer is not in the business of interpreting US/IRS code on when aviation taxes are/aren't applicable. They are here to facilities disputes resulting in services/goods not being delivered on the agreed upon terms with card member.

By having the ticket issued, you agreed on the amount to be paid for transportation and as long as you are transported to ticketed destination in ticketed class of service, JL fulfilled their end of the agreement. You were not overcharged as the amount on the JL ticket receipt matches exactly to the amount on your credit card statement.