First, those pilots are heavily trained and certified, far more than car drivers. And second, far more accidents occur due to humans than due to mechanical failure (and of "mechanical failure", only a subset of those involve incorrect autopilot, though I haven't found that broken out). http://www.planecrashinfo.com/cause.htm puts total human causes at 67% (53% of which is pilot error), and mechanical failure at 20%.

Some accidents also occur specifically when pilots ignore/override the automatic systems; I'd be interested to see statistics on that, too, but I haven't found any.