Cherry was not so silly as to think that Bob was perfect; she abhorred the violence between the Socs and greasers, and she truly liked Ponyboy and Johnny, although she felt helpless to fight the elite social structure in which she was firmly entrenched. However, she also seemed to understand something of human nature, i.e. she was more perceptive than perhaps the average teenager. She sensed right away that Johnny has somehow been hurt badly either emotionally or physically (when in fact it was both) and she understood that Bob's problems related to his upbringing or lack thereof. No one had ever told Bob "no" nor had anyone ever held him accountable for any social norms or boundaries, certainly not his parents, and in that sense, Bob was abused as well. He wasn't beaten like Johnny, and his outward appearance was such that everyone assumed his life was great, but anyone who's worked with teenagers for any period of time at all knows that they crave boundaries, even as they are fighting them, and Bob never had any.
There is a whole back story why Bob jumped on Ponyboy but what Cherry meant is he is special.