Rather than thinking the $1.50 is going to put more $$ in the store's coffers, I think it is to help the customer take ownership of the punch card, and be more pro-active about keeping track of and presenting the (one) card they have to be punched when they purchase something. If I paid for it, I will be more likely to keep track of it.
It could be pretty time consuming and frustrating to have to wait till the customer goes through her purse to find the 3 or 4 partially filled cards when she wants to cash them in. And easier for a clerk to cheat the system for a pal, if partially punched cards are accepted.