Neither CEA nor the Fund managers take any payment or fee from the Funds. CEA currently provides all funding for the project, because they think it gives many people a relatively high-impact way to donate.
At the end of 2020, Effective Altruism Funds began to operate independently of CEA. It will begin to conduct its own fundraising in 2021.
Note that some Fund managers may decide that re-granting money to CEA is the best use of their Fund’s money in specific situations (though they are not actively encouraged or obligated to do so). CEA has received grants (1, 2) from the EA Infrastructure and Long-Term Future Funds.