If there's some sort of logic to the way airlines price flights, then its lost on me, for sure. non-stops vs. connections, days of week, how full the flight is, whether they decide to sell more or less of certain buckets that day, or on the minute you purchase your flight.
Long story short, no one really knows. I doubt even if someone working in IM, if they could, would really be able to explain it. But basically, there are tons of calculations going on regarding how to best fill the flight while making the most $$. How many people are willing to buy at fare X, how many are willing to buy at fare X + $300, then at fare X + $500, and on and on. Basically, a computer is constantly predicting the best way to get the most money on each flight. Obviously, trying to sell all the seats at the highest price will lose them revenue because not everyone is willing to pay top dollar, and if they price too low, they'll fill the plane, but lose revenue because certain people are wiling to pay more.
If anyone can ever explain it fully, I'd be really interested to know. Doubt I ever will know, even in my next life.