It's not quite as literal as that. Apples-to-apples comparison would be used to describe a comparison between two things that are similar in nature, for example: comparing the acceleration of one mid-sized car to that of another mid-sized car. An apples-to-oranges comparison would be a comparison between two things that are not similar: comparing the acceleration of a mid-sized car to that of a bus.
"You've got to make an apples-to-apples comparison" is a widely used, if not overused, phrase in business. Tomandjerryfan gave an excellent example. Here's another one.
For example, let's say you are looking at a piece of equipment that cost only $10,000 to purchase but over its lifetime it would cost you $90,000 to maintain. You are also looking at another similar piece of equipment from another manufacturer that will cost you $20,000 to purchase but will cost only $60,000 to maintain over its lifetime.
You say: "I don't know - $10,000 vs. $20.000. It's difficult to justify twice the price for a piece of equipment that does the same job."
The salesman might say: "You have to make an apples-to-apples comparison, though. Sure, the other piece of equipment is cheaper to purchase, but you have to consider the cost to maintain it as well. Consider the TCO (Total Cost of Ownership) as a valid apples-to-apples comparison; our equipment will cost you $80,000 over its lifetime, while the other manufacturer's equipment will cost you $100,000 over its lifetime. You'll be saving $20,000, not spending an extra $10,000, when all is said and done."