I don't think anyone said everything he has done was good.
It's also not his job to handle Oakland and Tampa stadium deals.
I think the trimming of the minor league teams was great. The bloatin at the very bottom end of the minors, specifically rookie level leagues was pretty bad. Nobody needed a complex team and 2 rookie level affiliates plus more DSL teams.
Individual negatives aside, the game as a whole is in a much healthier and lucrative place for both the owners and the players since the start of his tenure, and fans are taking it in in greater numbers.
For context, the same could be said for Selig... and he was the biggest, scum-sucking POS human to be commissioner. Manfred presents at least somewhat likeable.