Upvote:4
As noted in the comments, and in many similar questions, airlines (and travel agencies) are desperate to conserve cash. Even large, full-service airlines have been extremely reluctant to pay cash refunds, using every possible kind of excuse to avoid doing so. In the US and UK, among others, they continue to drag their feet even after government regulators have made it clear that refunds are owed.
The customer has limited recourse here except to be persistent and to report the misbehaving party to its government and industry regulators, or shame them publicly through the news media or consumer advocacy organizations. If you purchased the tickets with a US credit card, you may contact the credit card company and explain the situation to see if they will issue you a chargeback.
There are hundreds of taxes and fees that may apply to an airline ticket, commonly represented as a two-character code assigned by ATPCO. They are not "prepaid" any more than your regular fare is, and so the travel agency's claim is spurious.
There is an official list of the codes published by the IATA, but it is a paywalled publication. Some but not all of the codes are listed on the Travel Insider blog; a more complete list is provided by Singapore Airlines, but this list omits which charges apply to which countries.