I have seen people hunting for the cheap flights at the last minute. When the time is less and there is a dire need to take the tickets, the people cannot afford to move around online or offline, sifting through the different websites or calling a number of offices of airlines. While there is urgency of flying on one hand and the need to do flight booking at low costs on the other, the service providers might not be in a position to offer last minute deals at low costs sensing that you do need these. For this reason, you might lose the advantage of cheap flights if you approach them offline.
By going online, you deny the service providers to sense your urgency of taking the tickets. Looking through the websites of the airlines could mean that you lose much of the crucial time since you will have to open multiple windows, reach the right webpage and make comparisons in order to ascertain which flight would be suitable. But, travel agencies have the data about all the flights from different airlines and their prices are sorted out for your travel requirements, facilitating easy comparisons and enabling you to make quick choices.
Another advantage is that the online prices mentioned by the agency are the prices at which the agency wants people to book. Since the visitors would be making the online booking and the visitors might prefer to have a look at other websites if the prices are kept on the higher side, the agencies always have this inhibition of pricing the flights on the higher side. The prices are kept in such a way that there is no room for price-bargains. In the scenario of doing cheap flights booking at the eleventh hour, this medium of online booking of tickets is a non-negotiating and time saving of effecting the booking.