Did you by any chance stop at a gas station and get spit on by a drooler hiding in the bathroom? That causes your character to become infected. If you remain completely uninfected, Jacob won't become a zombie after drinking your water
If I remembered it correctly, you have to stop by the police station at the beginning of the story. You will then learn about your saliva there after being examined by some crazy doc.
Then, that little guy will be saved. It also had cost me many playthroughs to figure that out.