Because their instinct doesn’t protect them against stuff not commonly found in nature such as cooked, mixed or processed food, as well as other animals humans have been unable to weight these pros and cons until the scientific advancements permitted it.
The fact that you can eat a whole lot more when a foodstuff is cooked is of course a con because you can then absorb it in detrimental amounts and overload the body. Then, being in a permanent state of overload, humans became unable to eat the same food raw, unmixed and un-seasoned since when they tried they bumped in their instinctive stop signals more or less immediately. As their were unable to understand this until recently (our nutritionists still haven't understood this), they had no choice but to keep on cooking!
Heat is thermal agitation. When heat accelerates the speed of the molecules, they knock against each other more and more violently. Thus, complex and delicate organic molecules can get damaged and transformed into innumerable new compounds of every shapes and kinds by chemical reactions with others molecules. Some of these new chemical compounds have been found toxic, some are mutagens, some are carcinogenic.
Google for AGEs (Advanced Glycation Endproducts), ALEs, Maillard's molecules.