In "The Catcher in the Rye," how are the people that Holden hates not innocent like Allie?

Holden hates "phonies," people whom he sees as hypocrites, and Allie certainly wasn't a phony. He admires his younger brother because he was so smart--just as he admires Phoebe. Because of Holden's sense of guilt about not being able to save Allie from leukemia, he feels a need to protect anyone or anything he regards as innocent, helpless, or victimized (Jane Gallagher, the nuns, the ducks in Central Park). The phonies he hates, on the other hand, don't need and/or aren't worthy of his protection. Stradlater, whom he both admires for his athletic prowess and success with girls and detests as a "secret slob"; Sally Hayes, his annoying ex-girlfriend he dates anyway; Luce, his old dorm couselor whose wisdom about sex he admired; Mr. Antolini, his English teacher he ultimately suspects is a pervert---all of these characters are phonies because they aren't what they seem to be, or in Holden's view, what they should be. 

Highly judgmental of other people, Holden cherishes innocence. Notice that those he wants to protect are mostly young or children like Allie. Holden has lost his innocence; he wants to save the innocence of the vulnerable ones. His choice of being the "catcher in the rye" reflects his goal.