Warren Buffet said it, famously, best: Price is what you pay, value is what you get.
And his words apply to buying airfares as to nothing quite as well. Low fares often come with a price.
Connections
I've seen fares to Asia via Atlanta with a 34-minute connection in Atlanta for hundreds less than fares offering a more sensible two-hour connection. Or sometimes the connection on a low fare requires an overnight stay in Houston, Miami, or Shanghai, at the passenger's expense. Sometimes this is a good thing if you think of it as "two cities for the price of one" and you actually want to spend 24 hours in Houston. But if you don't have a cousin or friend to stay with for free, it can add considerably to your real cost. Sometimes the lowest fares involve two or even three connections where a nonstop flight might be more but a much better value. If you miss a connection, you might not continue your journey for hours or days later.
Times of day
The lowest fares are frequently only available on red-eye flights or 5 a.m. departures, perhaps from an airport that requires a long drive from home. In order to make the trip work you might have to overnight at the airport the day before your departure.
Time of week
The lowest fares are usually available only for travel on Tuesday, Wednesday and Saturday. But many people who have limited vacation time can only travel on weekends, and those fares are often much more.
Seasonality
Seasonality is another value factor: a $500 flight to Europe in winter is not the same thing as a $500 flight to Europe in the summer. So a low winter fare is not the same "value" as the same price in summer.
Equipment
Airlines know that many passengers prefer flying on snazzy new planes like the Dreamliner or A380, with up-to-date entertainment systems, quieter cabins, electric outlets and WiFi, and they're willing to pay more for a better experience.
Airline
The lowest fares are often on airlines with iffy reputations such as Spirit, Aeroflot, or China Eastern. There's a reason why it costs less to fly to Zurich on Aeroflot or Ryanair than on SWISS.
Seats
If you wait for the lowest fare, the only seats available may be middle seats near the lavatory. Buying a fare earlier before departure often gives you a better selection of aisle and window seats.
Refundability/Changeability
Delta now sells fares that cannot be changed or refunded under any circumstances. These fares might be $40 or $50 less than fares that can be changed. American and United are rumored to be following this model, first launched by Spirit Airlines. Although it costs $200 to change a ticket, at least you might get something back if you need to cancel. These fares also require a fee to select a seat.
Fees
Southwest Airlines might have a slightly higher fare but there are no fees for checking bags, and if you cancel or change you get to use the value of the ticket on another trip without paying a penalty or fee. Frontier, Spirit and Allegiant even charge for carry on bags.
So while I'm all for low airfares, it's wise to consider not just price but the value of what you're buying and the quality of the experience.