The promise of aggregator sites such as Kayak is that you will get a look at all the options out there when you pull it up. Unfortunately, it’s not that simple and just as always, you need to shop around.
The problem is that no site lists every airline. Some of them (such as Southwest) don’t give their data to everyone. Others (such as Frontier and many international airlines) only give it to some of these booking sites. The best solution I’ve found is to use a site that aggregates the aggregators, such as Booking Wiz. Here’s why.
For two months I’ve been looking for a decent deal to Merida, Mexico the first week of January. Nothing, nothing, and more nothing. All of a sudden last week, when I went through the paces on Booking Wiz, I found a sub-$500 deal on Expedia, all taxes and fees included. It was ONLY on Expedia–not on any of the others, including Kayak. The probable reason was that it involves flying to Cancun, spending the night there, then making the other connection on Mexicana. Complicated, a bit of a pain, but worth it to save $200 and fly direct from my home city to Mexico. Expedia did some algorithmic magic to put it together, the others didn’t. When you try, CheapTickets may find your combination, while the others don’t. You never know, so keep looking.