Srobarts: I currently work for a small business travel agent. I can assure you that the vast majority of carriers pay 0% comm to us agents..We derive most of our income from booking and service fees.
For that reason, we'll book whatever our customers wants us to book - as long as within their company policy. Put simply, we get £25 per ticket whether its LTN/GLA on loco or LHR/NYC in F on BA
We have to keep an eye on the pax though - amazing how many will book outside of policy in order to rack up those miles...