He thinks she doesn't understand what's going on between them. To be fair, most people find her oblivious, marking her silence as confusion.
Usually, Brennan doesn't bother to correct the misperception. To explain her interpretation of the events would involve her reasoning, which she'd found most people would rather not deal with. Zack could, but Brennan's ideas concerning things like Angela's overenthusiastic response to mistletoe and sexless silliness don't really interest him.
Booth would listen, Brennan knew. He wouldn't follow the argument down into its intricacies, but he would listen to the explanation anyways, reading far more into it than she would want him to.
She isn't sure she wants to tell him, though. He can read into whatever he wants, but let him think her unaware.
She's positive that when she explicates the significance of a chip in a bone he's learning more about her than their case. If he knew that she noticed, would he look so hard?
She knows that he watches her, pouring over the bones on the table between them. She isn't entirely sure of what he sees, but sometimes he smiles to himself, like he's discovered something. Something about her, something that pleases or amuses him.
She'd been surprised to find she liked that look. That she likes shocking Booth. Once, she wore a low-cut tank top over a lacy black bra. She'd thought herself impulsive, but she had to admit later that it was for Booth.
Not for him, exactly. For her own amusement when he caught sight of the garment. She'd seen him, out of the corner of her eye as she leaned over the victim's ribcage to examine an unusual fracture pattern. Booth's gaze suddenly skittered away from her, his expression bemused, stunned, even appreciative. She relished his embarrassment, choosing that moment to call him over and discuss the victim's identity at length.
Sometimes, though, she's not doing anything particularly alluring when he tilts his head to the side and smiles. Brennan has seen her partner's eyes glaze over, like he's seeing another world, another life. When she calls his name he doesn't hear her for a moment, when he shakes his head and acknowledges her it seems as though he's coming out of a trance.
When he does that, she finds herself watching him back. More discreetly, of course. Still, every so often, her eyes meet his, and she feels the tug of reverie, the desire to slip into the warm chocolate of his eyes and never leave. The temptation to let the lab slide away and simply be in one another's presence grips her heart, and she must make an announcement to break the spell. An identity, an anomaly, even a lack of defining characteristics works, if said definitively enough.
He thinks she doesn't feel it, but she does.