Throughout most of the story Ponyboy believes his brother Darry thinks of him as a nuisance. He believes that if Sodapop would let him Darry would place Ponyboy in a boys home. Darry is always pushing Pony. "If he got B's Darry wanted to know why they weren't A's" "If they were A's Darry wanted to make sure they stayed A's." "If he was playing football he should be studying, and if he was studying he should be playing football." Towards the end of the novel Pony realizes that Darry loves him and the reason he is always picking on Pony is because he is afraid. Darry is afraid that he is going to lose Pony "just like he lost Mom and Dad."
As the story begins, it is apparent that Ponyboy considers Darry to be a leader and father-figure. As the chapters pass, however, Darry strikes/pushes Ponyboy much the same way their abusive father did.
At that point, Ponyboy runs off, much in the same way his brothers would when their father was present. What Ponyboy fails to realize is that Darry, as big brother, is still very much an adolescent himself, and is struggling to simply keep the family together, as seen in his dialogue about Ponyboy coming in at 2 a.m.; he responds with the threat that officials would "take them to the boys' home" if they didn't obey curfew.
During the beginning of the book Darry acts like Pony's father. He makes him do things that are good for him but Pony doesn't realize why he does that and gets all fuzzed up. The reason is he doesn't want Pony to get bad grades and not be able to attend college like he or Soda did. Eventually Pony ran away due to an accident that happened one night and soon they met each other and their bond became strong. The reason I think Pony thinks Darry doesn't like him at first because he kept acting like his father and acting like Soda's big brother. Maybe he didn't notice the reason I listed above.