It really depends on when you buy your ticket. Airlines assume, based on past load factors, how popular a route might be. If they expect it to be popular and have high prices but don't fill seats, they might lower them.
As Braniff747SP said, many shorter flights can cost quite a bit more, since they aren't a popular and less people fly, meaning the airline isn't flying a full aircraft and need to charge more to make money. Also, there might be less competition on shorter flights, meaning airlines don't have to fight for the business.
You are also going to find business versus personal travel. Most big business have an account set up and just pay what is advertised, where personal travelers will take advantage of Expedia, Kayak, etc to find the lowest price and airlines know that.