Benjamin should've gotten Lin's spot, without a doubt. It's a much more nuanced role, a much harder role to pull of, and he does it remarkably. I mean, didn't Lin's understudy get a better review than he did from the Times? Of course, Lin can do the role, it was written by him, for him, over the course of years. Even with that, Lin's emotions run from excited to awestruck to on the verge of tears. And besides, two other nominations that he for sure will win, the Tony voters couldn't thrown some bone at Benjamin.
AP I also think it was snubbed in the choreography and score categories.
"Hey little girls, look at all the men in shiny shirts and no wives!" - Jackie Hoffman, Xanadu, 19 Feb 2008