Countries participating in free trade are able to set certain rules for how trade is performed when dealing with that country. If they feel as though certain national interests can be protected through tariffs, for example, that is an option that they can freely exercise. Free trade is generally a good thing for any economy, as it allows necessary resources to flow freely between borders.
While free trade can often have certain economic benefits, especially for corporations, it often conflicts with national interests. For example pure free trade would not allow countries to impose tariffs in order to protect certain industries at home. Some industries such as steel, automobile, aircraft etc, have military applications. If such industries were to disappear, national defense could be threatened as a country would be completely reliant on other countries for such goods. This is one way free trade conflicts with national interests.