I don't believe Matt ever worked for SI. He was still in high school when he posted there as "Fatt Matt". He started up IHub in 2000.
He decided to skip college, and start IHub instead. I think he was strongly motivated by the fact that in 1998 the Dreyer brothers had sold SI for $144 million in cash and stock, and in 1999 Rusty Szurek had sold Raging Bull for about $350 million in cash and stock.
That ain't chump change. My guess is that he hoped to do the same, but the dot.com crash put paid to that.