Anger wasn't the reaction that John expected. Indifference, shame, or apologies would have fit John's expectations or observations. The storm in the Doctor's gaze gave him immediate pause. John was, after all, a man of outbursts. His entire life was an outburst, of sort, and nothing sustained.
His actual answer caught John even more off guard. He remembered 'Rose', of course, he'd had endless dreams about her, but they had been contextless...glimpses of adventures and that strangely haunting stare. He'd never even considered that she might have been the Doctor's...
He did remember waking up once and filling a page with failed attempts at scribbling roses, and that that need to find--or to draw or to have, he was never sure--a perfect rose. He'd thought it was just a particularly less lucid dream than most of his others. Perhaps it wasn't.
He wasn't really certain what to say. He opened his mouth to respond and nothing coherent came out for a few moments. Finally he managed actual words "I--I'm...I'm sorry...I thought..." Well, he'd thought Rose was just a figment of his imagination. A fantasy. It never occurred even when he realized the dreams weren't just dreams that she wasn't. Apparently this Doctor would already know that.
His dignity, however, demanded he collect himself somewhat. "You...you should understand, then, what it feels like to have someone insinuate that they loved her, rather than yourself."