In the case of Coke, I think the cost of packaging is bigger than the cost of the product, but either way its almost irrelevant to the price - they charge what people are willing to pay. I wouldn't buy a big bottle from a convenience store, a small bottle is more convenient for walking around with. I wouldn't buy a small bottle from a supermarket, I want a big bottle to put in the fridge at home.

Typically the smaller ones are also refrigerated whereas the 2L aren't, precisely because you're expected to grab the former when you're on your way from A to B and are busy.