Raito thought she was stupid. He thought that she had no brain to think with and that she didn't understand the things he did, or the things he said. He often had to explain the things he said to her as if she was a simpleton or a mere child. Half the things he said had double meanings, which she picked up on but would never reveal to him that she knew.
When he explained that he couldn't go on dates with her because of work, she knew that was the truth. But what he wasn't saying was that he also was very uninterested in going out with her to a restaurant, or to stay up in her room with her for a night, to talk- about her day, her career, their love- and maybe to even be affectionate and intimate like couples are supposed to be.
She knew that he was secretly relieved to be imprisoned by Ryuuzaki with their crazy working hours as part of the investigation team.
She knew these things.
She also knew that her boyfriend didn't love her. A man in love acts differently from the way he acts around her; a man in love wouldn't treat the woman he's in love with as a nuisance he keeps around for some reason. He had an ulterior motive to being with her. She knew this but she also was unsure what his motive was.
If he was truly in love with her, he would have been chasing her and begging Ryuuzaki to let them be together, even if it was for a two hours, instead of the one hour that they saw each other every once in a while when she threw a big enough fit.
Misa Amane also knew that the reason why Raito Yagami didn't love her was because he was in love with someone else.
The love of her life, and the man of her dreams-her Yagami Raito- was in love with Ryuuzaki, a.k.a. L, and in turn, he was in love with Raito.
She always had a feeling that something was off in their relationship. Two supposed friends trapped in a prisoner/master situation wouldn't have a spark of something that resembled romance between them.
Any time she came close to Raito, she noticed that Ryuuzaki stiffened up and had a hostile air around him, just as a dog acts when someone tries to take their favorite bone or toy away from them.
When she clung onto Raito and stared at his beautiful face, she noticed those quick glances he directed towards L.
Those glances read 'Help Me' and something more.
When Raito kissed her, she knew it wasn't for her. It was for L; to make him jealous. To make him want Raito more.
Just as Ryuuzaki plays his games with Raito, Raito plays them right back by using Misa as his deadly weapon.
If people knew that she knew about Raito's unfaithfulness and the tryst between him and Ryuuzaki, they would have thought her mad for staying with him.
Why would the talented and gorgeous Misa Amane stay with a man who treated her poorly, had no time for her, and used her for his own personal agenda?
The simple response would be that she loves him.
She trusts him.
She worships him.
He is her life.
Without him, she is nothing.
Because of her love for him, she would stay by his side and be the girl he thought he knew.
She did all this for love with hope that maybe one day, when L was out of the picture somehow, Raito would come to love her and they would live happily ever after.
For now though, she must play her part as Misa Amane, super model, actress, and the dumb girlfriend of Raito Yagami.