I'm sorry . . . there is an extra burden to all regional networks who decide to produce another program to displace an existing program be it News or something else.
Yes you're right revenue is paid on all programming, however they don't get to keep all revenue at any time.
This isn't a negotiated scenario as you suggest they should be better at . . . If a regional station enters into an affiliate program deal with a metro network, the regional stations do not get to keep 100% of their revenue. WIN, Prime and SCA negotiate accordingly, from 35% to 50% which goes to the supplier Nine TEN or Seven.
The extra cost burden to the regional stations is to find the money to pay for the news staff et al AFTER paying the percentage to the metros. The regional networks don't negotiate per program it is one in all in.
Some history for you . . .
It would be good to pick and choose the programs they want and pay accordingly, however once aggregation was approved through the Federal Government legislation back in the late 80's tabled by Paul Keating and Bob Hawke, the metro networks immediately offered their content as a one in all in scenario - hence you may have see all the historical articles supporting the demise of local production in all regional communities, encompassing the local children's television programs, women's magazine programs, local sport programs etc. etc. all because they had already paid for the content which would be displacing these programs.