If you use the Intercity Direct train service (between Rotterdam and Schiphol Airport, which you do if you travel between Rotterdam and Amsterdam), then yes, you need to pay the supplement in addition to your Altijd Vrij subscription. This supplement is not free, but costs 2.90 euros for a one-way journey, or 1.74 euros if you buy it by tapping your card at one of the red supplement poles on the platform.

If you often travel with Intercity Direct, you could also add “Intercity Direct altijd toeslagvrij” (always supplement-free) to your Altijd Vrij season ticket for 67.80 euros per month. This will allow you to use the Intercity direct train service for a fixed fee. If you’ve had your subscription for a month or longer, then you can do this yourself by changing it into NS Flex Altijd Vrij (which you already have), but selecting the “Intercity Direct altijd toeslagvrij” option in the process:
 

If you haven’t had your subscription for a month yet, you could contact customer service by phone, chat, X or Facebook and ask them to add this for you. Or keep paying the supplement for each journey until you can change it yourself.

Additional  to @Tochjo : You do not need to pay for the supplement when traveling with ICE inside the Netherlands.