Because there is more competition on the east coast, and the market forces them to reduce the airfare to remain competitive.
They charge what the market will take, there are entire departments in yield management who work out what they can charge per seat to maximise profit on any particular route.
The article by GT is discussing the general differences between costs on long flights and short flights and its effects on airfares, not market driven pricing.
Are you getting screwed, probably, can you do anything about it, probably not.