I have a flexible spending account card that also has mass transit benefits. It used to work on Amtrak.com (at least for trips that were around big cities in the Northeast, as that could count as commuting, for which the benefits were available). It stopped working, but I could just buy Amtrak tickets that qualified with my regular credit card and then submit the receipts or whatever to the plan administrator and then get reimbursed for them out of funds available in the plan, so in short, I was able to pay for Amtrak tickets with mass transit benefit funds.