Ponyboy's comment means Cherry correctly understood Johnny's true character, seeing his sensitivity and kindness beneath his greaser exterior.
When Pony says that Cherry 'sized Johnny up right' in The Outsiders by S.E. Hinton, he means that Cherry Valance has made an accurate assessment of Johnny's character.
Cherry saw beyond Johnny's outward appearance as a greaser and understood the kind of person he truly is: a sensitive and caring individual who has been hardened by his life experiences but still has the capacity for kindness and gentleness.
This statement reflects Cherry's ability to empathize and see the good in someone even when they belong to a rival social group.