Although Ben is Matthew and Callie's biological father, he hasn't always been around to take care of them. After he and Nikki split up, Ben basically just sends the child support check—but he's not there to provide actual emotional support or safety for the kids. Matthew reckons that this is because Ben is scared of Nikki, too:
I used to think that if Nikki was a tiger, then Ben was some animal that hides and scavenges; that scuttles about in fear. A giant mouse. (13.5)
But after Nikki gets arrested, Ben begins to understand that he cannot let his fear hold him back from being a good father. Just like Aunt Bobbie, Ben rises to the occasion and starts figuring out how he can protect the kids. Ben may be a little late to the fatherhood game, but Matthew, Callie, and even Emmy (who is not his child) need his help—and they're grateful when he takes them away from Nikki's clutches.