"Rigged" is such a...dirty word....
But look at Urinetown versus the enjoyable, but inferior Millie. Millie had as one of it's many, many producing entities a group of 40+ road producers/bookers, each of whom has one vote. Millie looked as if it would make more money on the road than Urinetown so there were about 60 votes for Millie right off the bat.
In a far more mediocre season, Titanic won Best Musical but the producers had said they were planning a tour. Again, all those road League members saw dollars if they booked a Tony winner, and that's part of the reason a so-so show in a rotten year took the prize.
It happens. Alas.
"If my life weren't funny, it would just be true. And that would be unacceptable."
--Carrie Fisher