"Wouldn't you hate the healthy?"
"Probably," Thomas said, glad he was on the immune side of things. (20.29)
Thomas is at first confused about why people would hate Immunes. Brenda explains: if you were infected with the Flare, wouldn't you have at least a little hatred for people who were immune to it? Wouldn't you feel a bit ticked off that you weren't born that way, too?
He keeps going and he doesn't stop, breathing in and out with the words that he hates. (21.32)
Despite working for WICKED, Thomas hated constructing the Trials. In one of his memory-dreams, a young Thomas recites the goals of WICKED, hating every word he's saying.
But all Thomas could think of was the angry boy throwing the knife that killed Chuck, that made the boy bleed to death on the ground as Thomas held him. (24.1)
Thomas hated Gally more than anyone else back in the Maze; after all, Gally was the one who killed Chuck. That changes in this book, after Thomas widens his perspective.
A bloodlust had completely taken Thomas over. He wiped his eyes on his sleeve, focused again on Janson's face. (72.11)
As you can imagine, hate is often channeled into other things—and in this case, it's channeled into pure violence and rage. Thomas uses all of his pent-up hatred for Janson to strangle the guy to death.