Why is cooking not potentially lethal?
Cooking is potentially lethal.
Just like how going out for a walk is potentially lethal (You could get run over by a car, maybe develop a stroke, or get hit by a meteorite).


Cooking or cookery is the art, technology, science and craft of preparing food for consumption.
 From this Wikipedia article on Cooking 

The basic idea behind cooking, as a whole, (regardless of the actual physical process) is to either make certain inedible (or indigestible) items  edible (digestible), or otherwise unsavory items more palatable.
Sometimes we have toxic substances that are rendered &quot;safe&quot;, through the reactions that the cooking process affords. Other times, the opposite happens.

Now, does cooking (boiling, frying, baking) something generate toxicants?
Almost certainly yes. But the amount and type of toxicant(s) produced is what determines the overall lethality of the item you've cooked.
The potato chips/fries we all hold so dear almost invariably contain acrolein and acrylamides, however in trace amounts. If, you chose to let the potatoes simmer for a little too long, then you'll better be able to taste the wrath of those substances.
It is the dose, that maketh the poison (as I've discussed in a previous answer).

The cooking process does, as you point out, initiate a gamut of reactions: Some simply break down the food into products you can better digest, absorb and assimilate... while others lead to products that aren't as useful.