Well, it was one company: the Peanut Corporation of America. Their plants were filthy and evidently the FDA doesn't have a budget big enough to hire as many inspectors as are actually needed. The exact cause hasn't yet been determined, but the two plants involved were hotbeds of bacteria, unsafe food practices, rats and rat feces, cockroaches, etc.
The peanut butter on your store shelves is safe. PCA sold their products to commerical kitchens like those in hospitals and to companies that make products with peanut butter in them, like peanut butter crackers.