The stat people that punch in numbers find it to be more profitable to offer layover trips cheaper than direct trips.
It costs more to have a plane from Pittsburgh and a second plane from New York fly to London, both less than 100% full of passengers. It costs less to have one plane fly from Pittsburgh to New York, where it will become 100% full on its journey to London.
Therefore, your layover ticket is “wasted” on you when you consider the alternative: you buying a direct ticket while also letting another stranger purchase (and fully use) that layover ticket.