That John is Elena's biological father never once factored into Caroline's thinking. Truthfully, the only reason she likes him is because he's alone. But Elena won't talk to him. (Elena won't talk to her, either, but that's only because she's with John.)
As a matter of fact, the only reason she's even thinking of Elena now is because she just realized that, in public, she would look like she could be his daughter. But she's not his daughter, and anyone who watches them closely enough could see that—not like they're together in public very often. He's not so cooperative then.
John doesn't love her—personally, Caroline believes he's still somewhat in love with Isobel, but he'll never admit that—and Caroline doesn't really love him either. Caroline loved Matt, but she'd never put him in danger by telling him about all the things that go bump in the night. And she loved Tyler too, but he doesn't trust her much anymore—not after she lied about so much. So she left and tracked down John because she needs someone to talk to, someone who will listen to her; and most of all, someone to hold her at night when she realizes once again that another day has passed and she hasn't aged.
He reminds her of this all the time—one of the only ways he can verbalize his dislike of the situation she has all but forced on him. "Are you sure you look old enough not to get carded?" he'll ask spitefully. "Don't you have school work you can do?" he'll say in annoyance when he wants her to leave him alone. The worst, however, is when he brings up her mother. "Are you going to go crying to your mommy now?" he taunts sometimes.
But she's the one with the trump card in the end. She just glares at him as she squeezes his wrist until he winces, reminding him once again who's in charge. Sometimes she'll even bring up Isobel, just to see that look of pain cross his face for a second before his eyes harden. She knows how much he regrets telling her about his failed attempt to get back with Isobel and she's not afraid to throw it in his face when he hurts her first.
They don't laugh together very often. There really is nothing funny about the situation Caroline's made for them. They're stuck in this little world where their only outlet is the one John hates and enjoys with equal fervor…and Caroline knows it.
John likes the fantasy of control, the illusion of revenge, as he pulls her hair and makes her scream. He likes to pretend, even for a moment, that what he does to her at night hurts her worse than what she does to him during the day. But they both know better.
In the end, she'll sleep somewhat peacefully and he'll lie watching her, unable to close his eyes right away. He can't help but wonder how someone so beautiful can be so cruel.
Caroline knows he hates her, and on some level, she hates him just as much.
He can't leave because she won't let him, and she can't leave because there's no where for her to go.