It's a contested topic, but my take is, as long as the manufacturer cannot remove the functionality of any already paid off features (be that via the original purchase, or via an add-on purchase later on), it's not a bother.
For those saying the hardware is already in there so it does not make sense to charge a higher price for the FOD, well... It's not that simple.
In terms of the marginal cost to install the additional software needed for the feature to function correctly, you are correct that this should be pretty low. After all, the manufacturer has already installed all the necessary equipment, the software has already been developed and paid for, and an additional minor fee to cover any installation / setup costs might seem reasonable from that perspective.
However, in terms of the average cost per car sold, things are more complex. First off, it makes sense that a manufacturer might actually realize savings from supplying all the required equipment for FOD in the car at purchase, even though they are not charging the customer for it at this time. This is especially true for widely requested and easily packaged options, such as heated seats, cruise control, smartphone integration, etc. The reason for the potential savings is that, once again, the marginal cost of equipping all cars with the said hardware may be potentially lower than actually setting up additional branches in the part sourcing, ordering and assembly processes in order to separate, e.g. cars with cruise control from cars without that, versus cars with heated seats vs cars without that, etc. Again, this would be especially true for any items that are widely requested by car purchasers, where the potential marginal cost of including said equipment is low.
Having installed all this extra equipment that a certain customer did not want to use per the original purchase order may have resulted in a net saving for the manufacturer, when taking into account the opportunity cost of not installing said equipment in the first place. That doesn't mean, however, that the manufacturer is not incentivized to continue seeking a positive return from supplying those items, be that when dealing with the initial customer or with any subsequent keeper of the car. FOD pricing is a means for the manufacturer to potentially recoup any extra costs associated with installing the equipment in the first place, and for realizing a net profit at that.
You may also think of it in another way. If the manufacturer only charged a minor fee for FOD due to the fact that all the equipment had already been preinstalled, then no one would have an incentive to buy the features outright. This means, however, that the manufacturer would actually provide all the FOD features at a loss, in terms of average cost per car sold. In the end, this would be unsustainable and lead to the removal of the equipment and FOD from future builds, or to a steep price hike for all FOD in order to ensure that the average cost per car is in line with the manufacturer's projections.