I am routinely screwed in the regard. For work travel, we have to use the corp travel agent, who usually books us into the lowest fare possible (for US domestic). Intl travel is in J.
Booking it through the website and getting reimbursed is not an option (in fact is in violation of my workplaces's travel policy)
In fact, I have to go out of my way to get on CO, usually by telling the agent, "I want to leave out of EWR", that usually gets me on CO, which usually ends up costing more than if I left from LGA or JFK.
A fact that the travel agent usually reminds me of.