In addition to bugs that can survive the pH of your stomach, there's also toxins in the food.

E-coli and such will produce toxins that remain in the food even if it's cooked/prepared in a way that kills all the live e-coli. That's why sometimes you get very sick after eating something but it passes quickly - you're just sick while your body purges the toxins out of your gut, but there's no live bacteria/viruses that take up residence in your body.