In short: Jerry Krause was responsible for breaking up the championship Bulls dynasty.

There was tension between him and the players, especially Jordan, because Krause felt he hadn't received enough recognition as the GM for putting the team together. The sentiment was that Krause was a very insecure person, and so having been the GM for the best team ever assembled, he really wanted to be acknowledged as the sole purpose for its success.

Jordan and the players acknowledged his moves in putting the team together, but they felt the team's success ultimately came down to the players on the floor actually executing, not just putting the team together.

Krause felt he didn't get the credit he deserved, so in 1998, he told the team that this would be their last year together and that he was gonna blow up the team, despite the team continuing to want to play together and compete for another 1-2 championships.

So that bitterness/spitefulness has never really been relieved because of "what could've been" in Chicago with Jordan and that squad potentially ending up with another few championships. Keep in mind they three-peated twice ('91-'93 and '96-'98).