Monkey D. Luffy didn't think like a simpleton, as much as most people believe it to be. His nakama certainly didn't think he was, and they never questioned his decisions—or if they did, the ineffably deep Roronoa Zoro would shed some light regarding their captain's inner mind. The fact that there was something more complex hidden past his straw-hat exterior was a major weapon used against his enemies. Their underestimation of the pirate king never seemed to fail.
But amidst all this, Luffy realized that even his mind couldn't comprehend the inner workings and thought processes of girls. One girl, in particular.
Throughout the voyage, his navigator proved to be much more than a girl who loved her life, her beli, her mikan, and—though she never admits it—her nakama. After having saved her from Arlong, Luffy thought a journey of this breadth would be enough to understand the thoughts that led to Nami's actions.
Then she left that message in the tone dial, and ran off again, spouting hurtful, faithless words. She led him to believe that she'd joined Shiki's crew, thinking that Luffy was powerless to beat him. He reasoned it was just a delaying tactic on her part. Or perhaps her deep care for East Blue blindsided her into believing she could barter a trade; her cooperation for the lives of her nakama and her hometown.
Nami never explained afterwards. When she pointedly told him that the tone dial was designed specifically so that idiots like him could understand, he'd tried to listen to the message again. But she'd successfully knocked it askew and into the sea. Whatever "hidden" message she'd left for him was lost under the power of the sea.
None of his nakama proved to be helpful, either. Luffy asked each of them what Nami meant, but most of them merely smiled and shook their heads. Sanji's heart-throbbing answers were typical, everything Nami-swan and Robin-chwan said were words of love. Zoro was no use; he thought too much like his captain, enough that whatever Nami hid away with her words was lost on him as well. But even then, Zoro still managed to shrug it off.
"She meant what she said, Luffy," the swordsman told his captain, his expression bored. He yawned, sat on the deck, and put his head down. "The message was pretty straightforward. No hidden meanings or anything of the kind."
Luffy tried asking her again, his frown deep and thoughtful.
"Nevermind, Luffy," she told him, her cheeks gaining a hint of red. "It's embarrassing. Besides, you guys saved me anyway, so there's no point keeping the message around, okay?"
"I said, no point," her eyes flashed, and he backed away. When he was at a relatively far distance (far enough away to avoid any surprise Nami-punches), she smiled. "Thank you, though."
The captain's frown turned into a puzzled look. "What for?"
Nami stuck her tongue out and turned away, back to her maps. "A number of things. Not leaving me there for one."
"You didn't think I could beat him," Luffy whined again.
"And for being an idiot," she laughed. "Close the door behind you!"
Monkey D. Luffy refused to believe that he was a simpleton. But he still needed to learn a lot. And he didn't think any long journey in the world would bring him closer to understanding girls. At least, one girl in particular.