I can't think of a current player where there is a bigger gap between his analytics and the popular conception of him. It's like a $5m player in one vision and league-minimum in the other.
He does think the game differently and does some bone-headed plays that stand out, and I think that's where the bad rep comes from.
The Ducks dumped him and a lot of Ducks fans said it was because of bad defense, but it never showed up in the numbers. And even Torts back in the day said that Milano's defensive game was fine, it was his one-man approach to offense (as opposed to cycling with teammates) that drove Torts nuts.
But then you've also got times like his Flames tryout where he didn't make one good play in several games, where it's hard to blame the team for passing on him. Sonny will have some weeks where his brain is just not in it. Some clubs will tolerate the bad with the good, some clubs do not tolerate the disappearing act.