Travel agents can, if they wish, charge fees for cancelling/changing reservations - over and above any fees that may/or may not be charged by operators.
They should have made you aware of any of any applicable fees at time of booking.
FWIW on one trip we were unable to use an hotel booked through American Express Travel. Even though it was a non-refundable booking we decided to do the right thing and cancel the reservation. Called the hotel direct: they said Amex needs to cancel. Called Amex: yes they would cancel booking, but it would cost £20. Needless to say we simply no-showed!!