It was his court, his team (the Bulls), his stadium, his fans, that were all in part being represented by that event happening. Its an ownership mentality that has rewarded Jordan extraordinarily well throughout his career.
His reputation and brand were all associated directly to whatever was happening to the Bulls franchise and happening in that stadium (which includes the fan experience). Now, Jordan might not notice if something trivial happens in regards to the fan experience, but something big enough to make the nightly news (and for which he was there when it happened anyway), he's going to take notice.
If they don't honor that, it reflects poorly on the Bulls franchise. This was a Bulls fan making a life-altering one in a thousand shot on Jordan's court. Jordan's on video celebrating with the guy. The fans, broadly, are going to be largely ignorant of the ins and outs of what was going on with the payout - what the fans know, is someone hit that shot and is getting screwed, and that it was a promotion that - as far as the average fan understood - was being put on by the Bulls. When it comes to brand, it doesn't only matter what's factually correct, Jordan understood perception. If that guy gets screwed out of his money, it might as well be the Chicago Bulls doing it (even if they put out press releases trying to disassociate in regards to responsibility).
When Jordan gets to the point and asks the winner: did you get your money? What he meant is: did those rat bastard businessmen pay you, because if they didn't, it reflects poorly on me, my team, my franchise, and I take that personally.
Pay on time? No.
Jordan's dark side includes people accusing him of millions in unpaid golf debts, bookies showing up dead with handwritten checks from Jordan, and the mysterious circumstances about his dad's murder.