Many have suffered while booking flights through agent sites like Makemytrip.com. The problems with cancellation or modification happens because it is a third party site and not at all related to the airline. They are only interested in taking money for a booking, not in providing after sales service. I have seen many reviews where users didn’t get refund when cancelling a ticket, or are charged much higher for cancellation than they would have if they had done it directly from the airline, or are not informed of the correct flight timing(especially painful if it is a connecting or transit flight) or are not informed even when the flight was cancelled days ago! Or worst still, being charged all the money but getting confirmation at the last moment or not getting confirmation or PNR and facing last day hassles at the airport.