Bruce loves Rachel.
That's why he can understand, as she walks away from the singed rubble of Wayne Manor, why she can't be with him. No matter how much it hurts (who knew having your heart broken hurt worse that having your bones broken), he'll always let her walk away. He knows Rachel couldn't be with a man like him, a man who put a masks on every day and makes himself look like a fool; like every other rich man out there who wastes his money on stupid parties, the latest cars, and exotic models. Who he really is is a man he never wants her to know, someone as good as Rachel shouldn't have to see what he has to do to make this city safe.
Sometimes he wonders if he underestimates her. When they were children, he would tease her, claiming she couldn't throw the ball as far as he could because she was a girl. She threw it farther. That seems like, to him, who Rachel is. She's stronger than anyone gives her credit for. He knows she can handle Batman, and inside he scolds himself for ever thinking she can't, but he doesn't want to let her. After so many times he had broken her heart himself, he doesn't want to do that again. Batman would. He knows Rachel deserves so much better.
Maybe things would've turned out different had he not become Batman. In fact, he knows they would. If his parents hadn't been killed, maybe his relationship with Rachel would be different. He's had dreams about these kinds of things, where he can finally give her everything she wants from him and everything ends up okay somehow, but that will never happen. As long as Gotham needs Batman, he can never be the man Rachel needs. No matter how much he wants to be, or how hard he tries, that man just doesn't exist any more. He wants to be able to be there for her, but he knows he can't, and sometimes he doesn't know what would hurt worst: abandoning Batman for her or adandoning her for Batman.
He knows she doesn't really understand (no matter how many times she says she does), but he loves her. That's why he's fine with that. That's why he understands (but not really) why she has to walk away.
Bruce loves Rachel. That's why that is what hurts the most.
