What are the characteristics that make Ponyboy unique among his friends?

Ponyboy is definitely a unique Greaser, and it's fairly obvious to the other Greasers—it's even obvious to people who are not part of the Greaser gang. This is why Cherry is able to so quickly and correctly analyze what kind of person Ponyboy is, shown in the following:

Cherry sighed. "You two are too sweet to scare anyone. First of all, you didn't join in Dallas's dirty talk, and you made him leave us alone. And when we asked you to sit up here with us, you didn't act like it was an invitation to make out for the night. Besides that, I've heard about Dallas Winston, and he looked as hard as nails and twice as tough. And you two don't look mean."

Ponyboy is unique among the Greasers because, at age 14, he is the youngest of the gang. He's athletic and smart like his two brothers; however, both of his brothers recognize that Ponyboy is exceptionally bright. It's why they are working so hard to keep him in school. They see that Pony has a chance for life beyond the gang and their rough part of town. Ponyboy is smart enough and well read enough to get an education beyond high school. Unlike the other Greasers, Ponyboy is a fairly open-minded and tolerant individual. It's what allows him to believe Cherry's statement that "things are rough all over." It's also why Ponyboy is able to see Randy as a fellow "guy" with similar problems.

"What'd he want?" Two-Bit asked. "What'd Mr. Super-Soc have to say?"
"He ain't a Soc," I said, "he's just a guy. He just wanted to talk."

Ponyboy has the innocence, vision, and ability to see beyond the black and white Socs vs. Greasers life that he lives in, and the other Greasers recognize this about Ponyboy. They all want to protect Ponyboy so that he can always "stay gold."