A California Bro and a down home Kentucky boy don't get along? No way!
I think it's mainly because Hopper drank his own Kool-Aid. The guy is talented don't get me wrong, but he was the highly politicized American addition to the grid. He was connected to the right people in racing, and found himself on the MotoGP grid in 2002. That year Hayden became youngest AMA superbike champion by beating Mladin on a V-twin RC51. Hayden's stock went through the roof, and his connections landed him on a works Honda with Rossi. Hoppers connections got him nowhere but wrecked in the gravel trap on a factory Suzuki. They were both supposed to have great careers. Both had pace, both got rides on factory bikes, both had world champs showing them around the circuit. But we know how it panned out.
From what I understand, Hayden sees him as a nuisance because Hopper is always trying to steal the limelight, a limelight that Hayden probably doesn't really want.
Now that Hayden is world champ it's probably even worse. I'm almost certain that Hopper left Suzuki because Nicky is world champ and Hopper wants his piece of the pie.
Their both vying to be America's favorite rider, it's probably not ever going to be amicable.