Many factors come into play. If the inbound connecting passengers number more than a few, then that's usually a very good reason. But not if they will make the outbound/waiting flight so late that it causes downstream problems. If there are more flights to the same destination, with seats, later that same day, then rarely will the plane be held. Obviously, with some international destinations this isn't the case, so the airline has to make the call whether or not to hold the departure or not (usually not if it will cause too long of a delay).

Every airline has an entire team constantly looking at late arrivals to see what effects they have on the passengers, connections and overall operations.