EDIT: Also, Christian Ponder is a better and more consistent fantasy QB than Brandon Weeden. Ponder has averaged 15 points per game and his worst game was 5 points, Weeden has only averaged 11 points per game and had a -1 point stinker in week 1. Ponder has had three games of 15 points or more while Weeden has only had two. And even if you exclude Weeden's first game, he's still averaging fewer points than Ponder.
The difference is in their receivers. Like you said, Ponder makes short throws. Short throws are completed more reliably (Ponder has one of the best completion rates in the NFL) and his top receiver, Percy Harvin, is an incredible yards-after-catch guy. Fantasy doesn't care if you get your yards by throwing deep or throwing short and running. Weeden's receivers have a bad case of the drops. Well, Greg Little does, I don't know about the others.
The one bright spot for Weeden is his team's defense is worse, thus forcing him to throw more. Ponder's worst game came in a win against Detroit because Minnesota had two return touchdowns and didn't need to try to come back from behind.