Because of Winn-Dixie
Opal really gets it when she says that her daddy, the preacher, "[reminds her] of a turtle, hiding inside its shell, in there thinking about things and not ever sticking his head out into the world" (2.14). He is a thinker, he's a hider, he's a sufferer who tries to forget his own pain and loss by focusing on his job. This makes him "a good preacher and a nice man," but not such a great father (2.1).
Here's the thing: it's not that he doesn't want to be a good father. He tucks Opal into bed every night. He listens to her stories. He loves her. But sometimes he forgets to do anything more because he's so wrapped up in his own pain. You see, when his wife left, "she packed her bags and left us, and she didn't leave one thing behind" (4.20). That's rough. And the preacher has never fully recovered.
He never tells Opal about her mother (until she finally asks), and though the church gossips had it right up in Watley—that "he's still in love with her" and "still hoping she'll come back," his lips are sealed. It's like he feels if he escapes into his job, his own pain will go away. But in the process he's alienating his daughter without even realizing it.
Enter Winn-Dixie. Not only does the dog penetrate his heart, but he also starts to crack the turtle shell.
Because of Winn-Dixie (yeah, you knew this phrase was going to show up at some point), Opal finds the courage to ask about her mother: Crack One.
Because of Winn-Dixie's sincere love and crazy antics (putting his head in the preacher's lap every night and catching without killing a church mouse—in the middle of a sermon!), the preacher starts to smile more: Crack Two.
And then get out your sledgehammer, because when Winn-Dixie disappears, he opens up a discussion between father and daughter that needed to happen (check out "Plot Analysis" for details): Crack Three.
Thanks to that discussion, the preacher's turtle shell pretty much explodes, and he realizes that his wife didn't take everything. He had forgotten "one thing, one very important thing that she left behind" (24.38). Yup, you guessed it. That "very important thing" is Opal, and when he realizes it, he exclaims, "Thank God your mama left me you" (24.40).
And so because of Winn-Dixie, the preacher becomes a daddy once again. A daddy who still misses his wife, but now, finally, sees his daughter.