Really.
"Did you know it was him?" <- That is Tony asking Steve if he knew that Bucky killed his parents (the "him" that Tony is talking about is clearly Bucky, the "it" is clearly referencing Bucky assassinating his parents)
"I didn't know it was him" <- This is Steve lying. He tries to claim that he didn't know it was "him" that did the killing (this "him", again, clearly being Bucky). With the way he's speaking, he's not denying about knowing about the assassination with this line, just CLEARLY lying that he didn't know it was Bucky.
"Don't bullshit me Rogers. Did you know?" <- This is Tony not believing Steve's half-hearted lie and asking him again if he knew Bucky was behind his parents' deaths
"Yes" <- this is Steve answering the question "Did you know that Bucky aka Winter Soldier killed Tony Stark's parents". He answers it with a simple yes. To put it into more words, he's saying "Yes, I knew (or had a strong hunch) Bucky killed your parents"
There are zero other ways to interpret that scene.