The short answer is "Yes."
All the fine reasons are given here: Zenyatta Has Earned Horse of the Year.
To those people who are insisting that the HOY always goes to the Classic winner, let me just point out that last year it went to Rachel Alexandra, and she never even ran in the Classic. Nope, it would be Zenyatta who won the Classic last year, but she didn't get HOY. Besides, this racing season, Blame lost to Haynesfield, and Zenyatta beat him in the Classic, too. And, the only reason Blame won (let's be honest) is that he had a clean trip and Queen Z did not. Had she only stuck her tongue out at the wire, she'd have won. Am I lying? Nope. She ran the better race by far. You just can't dispute that fabulous finish. She ran into traffic, and that's all about racing luck, not who is the better horse.
Regardless, history will remember Zenyatta. Blame ... well, not so much. Will the voting for HOY be fair? I guess we'll find out in January.