By the end of Safe House, I was led to think that Tobin Frost (Denzel Washington) was the good guy. That belief was challenged when he asked the other (good) guy to be better than him. Now, I am not a very careful viewer, so something along those lines may have been mentioned.
We are not really told exactly why Frost went rogue. But we can infer that this was because he was made a scapegoat:
Tobin Frost: I already am in your head. They're going to isolate you, Matt. They're going to be real nice to you at first. They're going to put their arm around you and tell you things like, "You did a decent job, son. We'll take it from here." That's when you know you're screwed. Forget about me, they're going to focus on you. They're going to try and make a connection between you and I. So that if this all goes wrong, they'll have something to fall back on in their little Senate hearings. I'm not your only enemy tonight.
When Weston asks Frost why he went rogue, he replies that it was because of all the lies. He mentions a specific case where (I don't remember exactly) someone in his charge is killed as he was about to reveal information about corruption in the CIA. Rather than doing something about it, Frost chose to keep quiet and thereby compromises his own integrity. He now wants Weston to do better.
In the epilogue, Weston tells his CIA boss (Sam Shepard) that he doesn't have any list. When he leaves, he tells Shepard that he'll take it from there and subsequently, releases the list to the press. Shepard is one of those on it.
If you really squint your eyes, you might be able to see a glimmer of an argument for Frost also referring to Weston's private life with his French girlfriend. He wanted Weston to not compromise his personal life for the sake of the CIA. In the final scene, the couple are reunited.