We, ie the US, have been involved in a negative ways in Central America in general, and in Honduras in particular, long before CAFTA.  The "Banana Wars", conflicts which involved the US in protecting US commercial interests in those countries date back to 1898.  Since then, we have routinely supported repressive regimes, often under the guise of fighting Communism, which have led to many of the current problems.  Here is one source:  https://www.boundless.com/u-s-history/textbooks/boundless-u-s-history-textbook/the-gilded-age-1870-1900-20/american-imperialism-164/the-banana-wars-905-8104/.
The Iran-Contra scandal was just one episode in our incessant harmful meddling.  And, then there is the School of the Americas, now under its "kinder, gentler" name:  Western Hemisphere Institute for Security Cooperation.....