Toyota has received exoneration from the U.S. Department of Transportation/NASA investigation of its control electronics implicated in a rash of "unintended acceleration" events—many of which are now attributed to driver error. DoT and NASA engineers examined the electronics themselves and more than 280k lines of code before reaching their conculsions.
This is not to say the company was not without fault in handling the situation, but chiefly in the way it may have been slow to respond
and with confusing statements. Buy then it was too late for the public to believe that recalls to replace floor mats that could foul accelerator pedals
or to add shims preventing pedals from sticking could simply be the remedies of problems in modern, electronics-laden cars.
But damage has been done to Toyota's reputation, as reflected in slumping sales. But other companies have rebounded from worse situations—the Tylenol poisoning comes to mind—with renewed attention to detail and demonstrated actions to prevent or drastically minimized such occurrences in the future—and there's no reason to believe Toyota will not be held in high regard in the future.
Meanwhile, now might be a good time to get a great deal on one of their cars with many of the incentives being offered.