Okay, so the gesture was kind of sweet, but it put a whole lot of pressure on Pepper and her relationship with Tony. It was a step Pepper just wasn't ready to take yet. Not that he was asking her to move in with him, but he might as well be. First he has asked her to leave CHOC and become COO of his company, which she did. Then he had moved out to Newport without asking her first. Yeah, Pepper was mad. The mad outweighed the sweet.
"What the hell, Tony?!" she exclaimed, all of those feelings bubbling to the surface. "You can't just spring something like this on a person! You're always doing that! Just stop! Stop!" She was getting flaily as could be seen by her hands.