Tony looked at Thor and said, "I think that you have a soft spot where Loki's concerned. I'm not deaf, I heard how you spoke about him on the helicarrier. Even if he's adopted you still consider him blood, and I think he has no qualms using that to his advantage." It may have been harsh, but that was how Tony felt. He only hoped Thor didn't attack him on the plane home.
He considered Loki in return for a while, then said, "were. You. In. Control. Of. Yourself?" If Loki hadn't wanted to kill anyone, or had only wanted to upset Thor, it might make him feel differently. Though he would never forgive Loki for killing Coulson.