Well, lots of things. First of all, I think she and Sherlock have a very deep friendship, and that no matter what, he can count on her and trust her, even if he's being an ass, even if he's drugged out--he knows she will be there for him and NOT because she's pining hopelessly for him but because he put his trust in her when his life was on the line. That alone created an intimate bond between them that could never be broken. She was there for him, believing in him in his darkest hour and he clung to that like a lifeline. For two years she didn't spill the beans. If he had died on his mission, she probably never would have said anything. Why put John through Sherlock's death twice?
The point is that she and Sherlock have an unstated intimacy between them (not sexual but deep friendship). He probably calls her often. Sometimes for a favor, sometimes to gossip. He expects her to pick up the phone when he calls, and I think it's a bit of a wake up call to him when she doesn't pick up every call. He's in a bit of a panic about her not picking up, but she's not in a panic.
He also knows flat out since ASIB that she loves him, that all the adornment she wore and the color of her lipstick and the color of the wrapping paper was all for him. And having her work with him for a day in TEH was like a date - Sherlock version - that ended with him wishing her a happy life when he acknowledged her engagement. Two ships passing on the night, but she declared out of his earshot that he was just her type. Still she carried on with Tom for another 6 months but it was clear at John and Mary's wedding that she only had eyes for Sherlock and that Tom was doomed. The writers could have had her go on with Tom and live happily ever after, but they didn't. They freed her up.
In TAB, much nonsense was made of Sherlock not knowing Dr. Hooper was actually a woman, people forgetting that Sherlock assigned her that role in his mind palace, and just as she had kept his secrets after TRF, he keeps that secret for her. He protects her. That's how he feels - protective of her since TRF. And at the end when the ladies are revealed in that cavern, she steps forward into the warm light by him but Janine only stays in the background, and Irene is nothing more than a picture in a locket. That warm light is very deliberate on the part of the filmmakers. This is how he thinks of her - warmly. This is his mind palace.
That's why he would never do anything to humiliate her in TFP, and Eurus' interpretation of it was from the POV of a psychopath. Molly knows he knows how she feels. Whatever happened that made her day bad was like her saying, "Really, you want to do this now? Why are you asking me?" She had to believe, however, that there was something more to the question or he wouldn't be asking it at all. Of course I'm not saying she thought that there was any kind of nefarious plot behind it, because she was oblivious, but for him to ask that out of the blue was something that likely triggered that ultimate deep friendship between them where he was saying yet again, "trust me." She could tell he wasn't playing one of his "stupid games." He was too serious for that, but she took control and made him say ILY first, and if he didn't say it like he meant it, she would not have said it back. That he said it even the first time made her smile a bit, but it was only after the meaningful second time that she said it. And that's not humiliation. That's actually her level of trust with him.