Padmé loved Anakin and there was no denying that. She would not have married him or fallen pregnant with his twin children if she didn’t. She thought the love they had for each other would be enough to bring him back which was why she followed him to Mustafar.
When she meets up with him on the volcanic planet, she begs him to run away with her and to raise their child someplace safe. However, at this point in time, he is so far past being able to be redeemed that he basically shrugs her off. It’s here that she realizes the man she married and the father of her child had changed to someone she did not recognize. It terrified her that the guy she loved and respected would kill innocent people just to prevent her from suffering a fate he could not control.
Did she think her pleading would snap him out of his outrageous thought process? Perhaps she did, but she was desperate. Her child needed their father and she wanted their lives together to continue. But given what Obi-Wan had told her, she would’ve known there was a slim chance to get through to him, but she had to try for the sake of her family.