If you are trying to find the lowest fare, put your dates into
farecast (apparently recently purchased by MS), it will send you daily updates and let you know if it thinks the fare is trending up or down. It also compares prices from the major sites against the airline (which is usually a couple of bucks cheaper).
Yield management and pricing are the secret sauce of the large airlines. Yield management is all about optimizing prices to stimulate demand and maximize revenue for each flight. Each empty seat is lost revenue, but underpricing seats is lost opportunity.
What throws a monkey wrench into the model is competitive behavior. As pointed out earlier, airlines will use predatory pricing to force competitors out of lucrative markets. Often you will see one major airline increase prices or fees, and if the competitors don't match, they will quietly reverse those increases. This
article is pretty simplistic, but is a start.