I think that giving the miles for making the connection is an incentive that the airlines offer to flyers to not take the non-stop along with in the majority of cases a lower fare to not take the non-stop.

The only way that the hub and spoke systems can continue to function effectively is with flyers going through the hub and not only wanting to fly the point to point flights. Remember at one time NW even gave bonus WPs for making a hub connection, not sure about other FFPs.

Since I am into the arbitrage of miles and taking the connections are beneficial for me the fare savings would have to be significantly more than they are now for this flyer to not take the non-stop if only direct mileage was awarded. YMMV