When President Carter said he wanted to set up a system of industry-style bonuses in government everybody who was anybody stood up and saluted.

Congress said the bonuses were a heckuva good idea and there ought to be a law. They passed such a statute with few dissenting votes. The Washington press, mostly, hailed the bonus concept as the greatest advance in civilization since Saran Wrap. Never was there a happier honeymoon.

But now that federal agencies are doing what the president and Congress told them to do, the cheering has stopped.

Two weeks ago The Washington Post ran a story questioning the application of the bonus system at the General Services Administration. The story noted, correctly, that six of 10 big winners were close associates of the admiral who runs the federal housekeeping agency. It pointed out that one of the big money winners was an old Georgia political associate of you-know-who! And that another big winner handled transition chores for the Carter-Mondale team.

Last week the Post ran a front-page story questioning the application of the bonuses handed out at the Small Business Administration. It noted, correctly, that seven of nine members of the panel that hands out the cash rewards themselves got awards. Nearly half of the SBA brass who cashed in on the awards, ranging from around $2,600 to $5,200 came from the special panel that picked winners. In its defense, SBA said that when it came time to vote on awards for panel members, those members left the room.

There have been similar questions with new merit raises and bonuses at the National Aeronautics and Space Administration and other agencies.

The problem people seem to have with the system is not the bonuses themselves, but who got them, and how they were selected. The implication is that favoritism has reared its ugly head, that perhaps people who are in charge of the program, or who are close to the boss, got the awards. The "surprise" is that people who are boat rockers, or non-team players, or not perhaps properly politically pedigreed did not get the awards. That seems to be what has surprised Congress, the public and the press. What surprises me is that anybody is surprised! What did we expect?

The bonus and merit pay system in private industry -- which is not nearly as widespread or lucrative as bureaucrats imagine -- is far from perfect. If you think that favoritism, politics and social or personal connections don't count you were probably raised in a nunnery.

There is the argument that merit and productivity are sometimes easier to measure in private firms where products are produced, or not, and, where profits can be measured by the dynamic -- or dumb -- action of some executives or corporate veeps. There is also the argument that foul-ups and favoritism are not so bad in the private sector since people can boycott products and stockholders can protest or refuse to invest. Stockholders in the U.S. goverment don't have those options.

It appears that we -- the public, press and Congress -- like the idea of running that government like a business, with bonuses and all. But we don't want the human factor, favoritism in any form, in the system. If that is true there are two very simple solutions:

A) Drop the bonus system. There are a lot of people around who think that having an important government job, and earning $50,000 per year, is its own reward. Why should the public be forced to subsidize cronyism any more than it already does? If you are a high fed and think you could do better in the corporate world, be my guest!

B) Find a perfect bonus system somewhere and adopt it for the government. Should we turn to General Motors? Or the Bendix Corp? Does the military always promote the best man (or woman)? How would the State Department job reward plan?

Maybe we could turn to that most democratic of systems, American politics. Does it always produce and reward the best? From a vast talent pool we must choose among Jimmy Carter Ronald Reagan or John Anderson.Maybe we should reconsider option A.