flufdriver,
How a scrupulous agency will make it's money is by negotiating the best available deal, for the crew member, with the airline. The agency that offers the best T&C's will get the crew members and other agencies may lag behind.
It is a common complaint, amongst crew members, that agencies are 'stealing' their earnings, an agency may work on a one off placement fee, a percentage or a fixed monthly fee but that rarely comes from the crew member's earnings, more often than not the airline pays the agency fee.
As an example, and other countries are higher, in the UK for an airline to employ the crew member directly will cost the airline 12.8% in employer's National Insurance contribution. If they recruit contract pilots via an agency they are perhaps paying the agency, not the government, that 12.8% thus the airline have paid the agency fee.
Whilst the self-employed contractor will thereafter be responsible for his/her own self-employed NI contribution this is an insignificant amount set against the tax deductable advantages of being self-employed rather than employed.
Of course, an agency can only offer the best T&C's that have been made available to it but that's life!