The S&P 500 was 1300 when he sold to Yahoo. He received $1.4 billion of Yahoo (14.6m shares at $95/each). He had to pay taxes on clearing out that position as well, so you can safely assume his after tax position was more like ~$1.1 billion. He very solidly beat the S&P 500.
He's worth $4.08 billion today according to Bloomberg (ranked #500 on their global rich list). He has increased his net worth by nearly 4x.
The S&P 500 is at 2747. It has just over doubled since April 1999. He'd be missing a billion dollars if he had gone with the S&P 500, including any dividends.
He was better off with what he did, he beat the S&P 500 index fund. Not only did he make more money his way, he got to do what he wanted to with his money, such as buying the Mavericks.