The WCW fans were booing Hogan a bit since he went there in 1994. WCW had a different style and fan base and Hogan never really got over with them like he did in the WWF where it has always been more entertainment based as opposed to WCW which was a more wrestling based product.
Hogan's act was growing stale with the WWF audience as well. Before he left in 1993 he certainly wasn't getting the reactions he used to. Also, the fans really got pissed at him after what happened at WrestleMania 9 when after Yokozuna beat Bret Hart for the title, he came out at the end and beat Yoko for the belt in an impromptu match that made no sense. It was no longer Hogan's time and he didn't need the belt. The WWF was starting to build around Bret Hart as the top guy and Yokozuna as an unstoppable monster, so Hogan winning there shouldn't have happened and that's really where fans started to sour on the Hulkster. Fans were even turning on Hogan a bit in 1991 when he feuded with The Undertaker but WrestleMania 9 was when people really started to turn on him. Also, by 1993 the kids that had loved Hogan in the 80s were now growing up and liked different things in wrestling.
We should talk history more often in this thread. It's definitely better than what's going on in wrestling now.