Free trade does ensure that transportation costs are higher than they would be otherwise, however it enables a centralization of manufacturing, which is often a larger source of pollution. This means that rather than every country making everything themselves, each country instead makes what it can most efficiently make, thus using fewer resources in production, and reducing pollution in this efficiency.
With more businesses being created in the natural resources trade, there are a variety of concerns being created. One, for example, is that this constant trading of oil and other minerals needed for everyday life is being stretched to thin which will have a negative effect on our planet's environment. Eventually, the constant abuse of natural resource trade will leave the countries in a state of scares resources, which could, in turn, cause economical issues as well has natural ones.