Every time I have to handle a penny it wastes my time and energy for no gain. I never find having a penny useful unless it will prevent me from getting more pennies. Multiply that by everyone in the country and that is quite a waste of time (i.e. money). There would be almost no loss of economic efficiency if we get rid of pennies but a nice savings in real time and energy, to say nothing of the waste that mining, refining, stamping and distributing them costs.
Even if you were being short changed at every purchase, assume 10c being the smallest coin available, you loose worst case 9c per transaction, assume you make 2 transactions per day. That's total $5.4 lost per month, I can live with that. Especially since it's a worse case scenario, realistically it's +/-0 and even if merchants have a special secret method for winning they can probably only win 5c on average making the loss half of my worst case scenario.