Many consumers assume that their favorite airfare booking engine or "aggregator" includes fares on all airlines. This simply isn't the case.
Airfarewatchdog researchers have found that some sites exclude certain airlines, either because these airlines only sell seats on their own site, or sometimes because the airline refuses to pay the aggregator or online travel agency (OTA) a fee for listing its fares.
This can change over time. A site may list an airline temporarily in order to demonstrate the financial consequences of being delisted, but usually the banished airline won't budge anyway. (JetBlue's fares seem to come and go on Orbitz, for instance.)
Alternatively, an airline may add or remove its fares owing to a dispute over commissions. A couple of years ago, United's fares mysteriously disappeared from Travelocity for several weeks. This could well have been because of a commission spat, but Travelocity did not offer an explanation as to why it happened.
It is quite possible that Virgin America's fares will be popping up on more sites in the future as the new carrier gains traction.
Kayak has been playing a cat and mouse game with Southwest over the last few months. Southwest's flights, but not its fares, will pop up briefly and then disappear in a flash when doing a search from, say, Baltimore to Fort Lauderdale, a route that Southwest flies. You'll see an "info" icon but no prices or other information. (Southwest explicitly prohibits other sites using its Web site to mechanically "scrape" or monitor fare or other information.)
Here is a partial list of airlines that are excluded from the fare listings of various online airfare booking sites:
Orbitz: Sun Country, JetBlue, Southwest, SkyBus, Allegiant, USA 3000
Travelocity: Southwest, SkyBus, Allegiant, Virgin America
Kayak: Southwest, SkyBus, Allegiant, USA3000
Expedia: Southwest, SkyBus, Allegiant, Virgin America, Spirit, USA 3000
Sidestep: Southwest, SkyBus, Allegiant, Virgin America, USA 3000
In addition to this list, it's important to note that many international, and some U.S. domestic, airlines reserve their best fares for their own Web sites, even if they do list most of their fares with third-party sites.
For example, even though Spirit Airlines lists its fares with Expedia, you won't find its 1 cent, 2 cent, and $1 fares listed anywhere but on Spirit's site. Alaska Airlines lists with virtually all OTAs, but has frequent 20 percent-off sales that you'll find only on the airline's own site.