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The Cheapest Flights Are Not Always Available From The Airlines
You may think that you will find the cheapest flights directly from the airlines, but this is not the case. Airlines often sell seats in bulk to online travel agents, in what is called consolidator fares, and they do so quite some time in advance, meaning that they can offer the lowest possible price to the online travel agent. This means that they will have fewer of the cheaper seats to sell on their own website. In some ways this is good. Many of the best online travel agents will sell the cheapest flights directly to you without any booking fees, whereas when booking directly from the airline, you may find yourself hit with fee after fee, some of which are completely and utterly ridiculous. Now, an online travel agent cannot get rid of these fees entirely, but they can limit the ones such as booking fees, or the charge for speaking with a human being.
And this is one of the advantages of booking with an online travel agent. They will take the time to speak with you and will not charge you a fee for the "pleasure" of speaking to someone who can actually answer any questions that you may have. It's hard to imagine that the airlines themselves would not want to drive traffic to their website by offering the lowest fares there, but they have the advantage of possibly selling more tickets when they offer these seats to a variety of other sites that can resell them for the airlines. It seems like a win-win for everyone.