For one thing not everyone walks around with pennies in their pocket. So supplying the penny would help in sales that otherwise would not happen.
For another, use price to capture value (perceived or real) and not to offset your costs.
Or they read the 1% Windfall and decided to increase price by 2%.
Most likely they did this due to operational reasons, stocking pennies and keeping it replenished. With customers supplying their own the machine will continue to generate sales without restocking.
But again why let your operational inefficiencies become a cost for your customers?