The main reason that it's not recommended to eat meat that's been allowed to grow bacteria (even if you plan to cook it) is to avoid the toxins produced by Staphylococcus aureus:
Man’s respiratory passages, skin and superficial wounds are common sources of S. aureus. When S. aureus is allowed to grow in foods, it can produce a toxin that causes illness. Although cooking destroys the bacteria, the toxin produced is heat stable and may not be destroyed. Staphylococcal food poisoning occurs most often in foods that require hand preparation, such as potato salad, ham salad and sandwich spreads. Sometimes these types of foods are left at room temperature for long periods of time, allowing the bacteria to grow and produce toxin. Good personal hygiene while handling foods will help keep S. aureus out of foods, and refrigeration of raw and cooked foods will prevent the growth of these bacteria if any are present. — Aggie Horticulture: Bacterial Food Poisoning
And, remember: this is just one malady. The link gives a few other examples of bacteria which produce nasty things that can survive cooking, though usually they're not found on meat but other types of food.
And if you found the meat outside (e.g. roadkill), then it's even risker to eat, especially if it's rotten. You would have no idea how the animal was acting before it died, and you may not even know why it died or how long ago. Plus, staph (not to mention other bacteria) can be found in any number of animals: wild animals in Spain, bushmeat in Tanzania, goats and sheep.