Neat chart from Horace Dediu. You can think of the price-earnings ratio as a measure of financial market optimism about the future. By the autumn of 2009, the S&P 500 had settled into a low-PE ratio, high-pessimism point from which it's been slowly recovering.
Apple, meanwhile, spent that time as a company that not only had high profits but about which there was a lot of optimism about earnings growth. More recently, though, the market's view is that Apple will grow slower than the average company over the relevant time-frame.