Free trade agreements with less developed economies result in a natural movement of capital from the wealthier economy to the less developed one - lower capital concentration in the poorer country makes capital more profitable there than in the wealthy country, and dropping trade barriers generally makes it easier to re-import profits.
In the very long run, the economies of freely trading nations will tend to converge given similar patterns of private savings, education, etc, but as famously state by John Maynard Keynes (and perhaps the only thing he ever said correctly) "In the long run, we're all dead."
So for example, the Canada/US free trade pact had the potential to be mutually beneficial, as the involved countries were at similar levels of economic development. Similarly free trade with Western Europe would probably benefit both the US and the European countries. Free trade with less developed economies, like Mexico (NAFTA) and the CAFTA pact will hurt American workers, especially at the unskilled-labour level, for at least a generation, and probably longer.
Don't get me wrong, the pact will result in economic growth, but the gains will accrue to capital owners and highly skilled workers, as well as unskilled labour in the poorer countries.
I'm not a big fan of protectionism, but I am a big propnent of 'history matters' and tend to believe that slowly dropping trade barriers is less risky to the stability of an economy, and preventing the degradation of income for less skilled workers in the wealthier economy. It's a significant conflict of interest for government, finding a balance between protecting the livelihoods of a large group of its own citizens, versus dropping trade barriers which, in the long run will make everyone 'better off'.