Free trade is only desirable to the stronger economy/ies in the bloc. For example: The Eurozone benefits the already established industrial powers (Germany) while giving no incentive for the smaller countries to set up their own factories.
Then how come that smaller countries in the EU seem to thrive economically?
In a free trade agreement, Germany can now dump all of their products in a smaller country and take all of their money. Germany doesn't need to buy anything from them: they already make everything their need - so basically the smaller country is just a raw material supplier, or purely agricultural exporter.
Germany as a whole does not decide that it needs not to buy anything from, say, Austria. It's individual people or corporations who decide to buy from supplier A, B or C. In a free market, supplier C from Austria has the same chance of being chosen as A and B from Germany.