I assumed the reason for this was simply about incentivizing people to book directly, while penalizing people who rent through an agency (such as Priceline), si

I assumed the reason for this was simply about incentivizing people to book directly, while penalizing people who rent through an agency (such as Priceline), since those agencies generally offer lower to much lower rates to you, plus Hertz then has to pay a nice commission to the agency, further destroying their margin. Reason for my assumption: you are unable to add your hertz account to a reservation done through a third party, meaning those people always are forced to wait in the lines and use the counter.