That's a pretty superficial analysis of both Hughes and Yankee Stadium.
Hughes is basically the WORST kind of pitcher for that stadium. He's a righty, which means lefties have an advantage against him. Which means lefties also get to take advantage of that stadium's ridiculously short RF porch. While not horrible at missing bats, he's not particularly good at it either so that doesn't help him out.
And Hughes is a flyball dominant pitcher. Of course he's going to get killed in New York. He has almost the exact opposite profile of the guy you want pitching in that stadium... Everything about that place is working against him.
Comerica & US Cellular say hello...