TAC On,
There is some truth to what you say but not all.
Agencies can work to either a fixed fee, X amount of dollars per month or they can work on a percentage.
You seem, if you don't mind me saying, to have a chip on your shoulder that the agency are taking this amount of money from your salary, rarely does that happen, it is common practice that a fixed amount, or a percentage, is added to the salary and this is incorporated into the charge rate to the airline.
To explain this a little further, and as an example, if you are employed directly by an airline in the UK then they need to pay, on top of your salary, 12.8% NI contribution to the government. If you are employed via an agency then they would now have 12.8% in the kitty to pay the agency fee.
That 12.8% could never be claimed as part of your salary if it now paid to the agency and as a contractor you would be self employed thus the agency are not required to pay 12.8% to the goverment thus perhaps, just perhaps, this is where their fee comes from and not from the pilot salary.
To agree with you on another point however, Airbus Jockey is incorrect to say, to generalise, that contract pilots are paid more. Perhaps they may receive more in their hand but thereafter they are responsible for their own taxation, NI etc. and this brings it down somewhat.