The problem with that argument is that those connecting passengers are often paying a lower fare, to go further, than the O&D passenger. For example, for Sep 20, the current BOS-LGA fare is $304 while the BOS-LGA-PIT fare is $149. If the airline was getting more revenue from the connecting passenger, your argument of setting aside seats for them would make sense.
In an earlier thread, the same pricing issue was true for PIT-HPN vs LAS-PIT-HPN. The passenger connecting in PIT was paying about half what the PIT O&D passenger was, to ride the same airplane on the PIT-HPN segment.
When the revenue is half as much, to carry the connecting passenger more than twice the distance plus the added "handling" cost of the connection, something is screwy as far as the customer is concerned.
Jim