When he was taught by his father to hate homosexuals, Ennis was taught to hate his own feelings. Years after he first makes love with Jack on a Wyoming mountainside, after his marriage has failed, after his world has compressed to a mobile home, the laundromat, the TV, he still feels the same pain: "Why don't you let me be? It's because of you, Jack, that I'm like this -- nothing, and nobody."
I think his father was trying to teach him to be a homophobic, not to hate homosexuals.