I recently had a bad experience with one of these 3rd party online “travel agents” (JustFly) and after researching more it is quite apparent that some of these companies have highly unethical business practices. Hopefully my experience can help others avoid being scammed as well.
The issue I had with JustFly is that I had to cancel a trip to Mexico last minute. They offered a “full travel credit” but required a $150 cancellation fee. I paid the fee and received a credit of about $457. When I went to rebook my trip, both directly through JustFly, as well as through Kayak, I found another flight, same origin and destination, for $407. When I tried to book it on JustFly, I was not able to use my travel credit, I had to use my credit card. Turns out in order to use my travel credit, I had to book through “My Bookings” which leads to a different flight search. I found the exact same flight, as on Kayak and the JustFly website (which was $407), offered to me for $660. They were adding a $253 mark up just to use the travel credit! JustFly is running two different flight search engines on their website, one for credit cards and the other for travel credits, and jacking up the price on travel credit purchases since those customers cannot shop elsewhere.
Do thorough research prior to booking with any travel agent or service other than the airline directly.