How do I get my players more interested?

Kill them all, and rip their character sheets up in front of them while maniacally laughing, so as to establish dominance!

Ok, so that's all terrible advice as you know. I would first try and see if the player that is very into the story can help bring them in. Given that the story is already underway, I'm not sure how tied the character's backgrounds are, but that is one way to potentially help the active player bring in the less active ones. The player that avoids the story will likely need their personal stakes in the game raised, but that may be difficult as well. You already mentioned that piece. If possible you could play the quantum ogre game, in that when the player strays they happen to stray into things that would most likely lead them back into the story. Those are just a couple potential ideas that may help, but I'm sure other people have more.

The problem with indulging the anti-story line player is that she tries to derail any story even if it is based off of something she has done, for example, in the fist city that the party arrived in she went around threatening shop keepers and guards until she was thrown in jail. All said and done she had amassed a bail that would have wiped out most of her remaining gold to pay off, several hundred gold. Because of a high will save she overcame the silence spells placed on her, so she spent her time in jail screaming insults at the guards. By the time her court date had arrived the party had been split for about a session and a half. So I created an ad hoc dungeon to clear as community service, and had the judge recommend that she bring her friends. This was met by a chorus of train sounds as she wanted to continue on alone, but the split party was causing problems with the other players.