The theory of factor market distortions deals largely with taxing inputs. However, input subsidies are not only common in manufacturing. For example, U.S. agriculture is heavily dependent on input subsidies.
If water subsidies in the production of California cotton were removed, along with commodity payments, production of cotton in California would likely cease. Likewise, transportation subsidies were common in both the U.S. and Canada, and still prevail in the U.S.