Officials of one of the nation's large fast-food chains and the president of the Michigan Association of Home Builders have decided to make their complaints about the Reagan economic program felt where politicians are most sensitive: campaign contributions.

Executives at Shoney's Inc., "putting our money where our mouths are," have started an openly anti-Reaganomics political action committee.

Gerald Kosminsky, the Michigan homebuilder, has notified GOP leaders that he is withholding all Republican contributions because "I simply cannot support . . . political candidates who cannot or will not assist in the survival of our industry."

"We are advocates of the free enterprise system," Michael Skelton, vice president of Shoney's--which owns 350 restaurants and franchises another 550--said in a telephone interview from the firm's headquarters in Nashville. "You would think a Republican administration would also be an advocate of the free enterprise system."

In a letter to members of Congress respresenting districts with Shoney's restaurants, the company said current economic policy is like "two trains heading on a collision course." One of the trains is the Federal Reserve's tight-money policy, while the other is "engineered by President Reagan and his economic advisers, who seem intent on increasing the money spent on defense and maintaining an extremely large deficit."

In an unusually declarative statement, the firm told members of Congress, "In our solicitation drive, which is not yet completed, we have accumulated approximately $75,000. This money will be spent as our steering committee deems appropriate to those individuals and organizations that best represent our interests and the overall interests of the free enterprise system. "Interest rates have got to come down, and the federal deficit has got to be eliminated."

Skelton said the firm has not yet set out a legislative agenda, but it clearly would not be a return to spending programs as a replacement for Reagan's tax cuts. The chain does appear to support strongly reductions in the defense program, however.

In a separate action, Kosminsky wrote to Rep. Guy Vander Jagt (R-Mich.), chairman of the National Republican Congressional Committee:

"As an association, we supported President Reagan's economic package last year almost unanimously at the National Association of Home Builders board meeting in Washington, D.C., but now the same policies are forcing my colleagues into bankruptcy and in a lot of cases with life savings thrown right down the drain.