There's poles on platforms the IC Direct leaves from you can scan your card at to pay the supplement. You do that in addition to checking in and out. This works with an ov chipkaart and according to https://www.ns.nl/en/customer-service/payment/ovpay.html it should work with a credit or debit card the same way just fine.

Of course, you can also buy the IC direct (Schiphol - Rotterdam) supplement online https://www.ns.nl/producten/en/s/intercity-direct for € 2,90 or at a ticket machine or NS service desk with a € 1,00 surcharge.

Using the red pole at a platform will save you 40% in off-peak hours.

To avoid the surcharge/supplement altogether, feel free to take any other IC train to Rotterdam (via Leiden, Den Haag) which will take about 40 minutes extra).

If you activated the IC direct supplement and decide (or forced because of outages) to take a regular train, you can cancel the supplement/surcharge by tapping your card at the pole again within 30 minutes https://www.ns.nl/en/customer-service/termination-cancellation/cancelling-a-supplement.html