That's because you cannot patent foods. You can only patent a method for making food or the recipe, which brings to mind the concept of a "trade secret". Coca-Cola has been protecting its trade secret on the Coke formula for over a century because filing for patent protection requires that you reveal the formula. That's the price that you pay for your 20-year "monopoly". Instead, Coca-Cola locked its formula in a vault and hasn't let any trade partners or joint ventures even take a peek. Sure, they let independent bottlers produce the end-user product, but the Coca-Cola corporation is the sole distributor of the syrup.
Yes, PepsiCo has been able to rise to prominence despite Coca-Cola's corporate "isolationism" in protecting its Coke formula, but that's only because it's fairly easy to reverse engineer an adequate simulation of flavor of soft drink.
But imagine something like drugs, which are far more difficult to reverse engineer. If we didn't have a patent system that gives companies a small window in which to be sole distributor BUT forces them to reveal their trade secrets, then every pharmaceutical company would lock up their formulas in a vault like Coca-Cola does. Imagine Bayer being the only manufacturer of aspirin for over a century? Today, I can buy a bottle of aspirin for less than a dollar. How much would it cost if Bayer still had a monopoly on aspirin?
The choices are: what you call "government-sanctioned" monopolies for a fixed period of time OR "corporate isolationism-based" monopolies to perpetuity. Which scenario do think stifles innovation?