Several things pass through Souji's mind as he listens. The first is that it really isn't Chara's fault. But they're not going to listen to that mess - it's too much of a platitude to mean anything if he should say it.

The second is that it borders on arrogance to think that they are the sole cause for whatever's going on with Frisk. Frisk certainly plays a part in it, willingly or not, and Frisk is the one who chooses their own actions, events notwithstanding. So to think that all responsibility lies with Chara is self-centered in that it's egoistical. But he doesn't think saying that will help, either.

Then again, he's fairly certain that nothing he says is going to help. He probably isn't in a position to provide real help in the first place.

Then what can he do? What can he do other than speak his mind and make sure he's there when he's needed?

"I think you're giving yourself a little too much credit." He leans one hip against the counter, arms loosely crossed over his rib cage. "Frisk also has something to do with their situation."

Frisk has determination, which means that they aren't simply a passive player in their own lives. At least, that's how Souji understands determination. There are a lot of things in their world that don't mean what they mean in his.