I am interviewed in this article and have been a close observer of the situation in Honduras since 2011. Many of the concerns raised in this piece are legitimate.
However, Paul Romer's involvement and renunciation do not indicate what people think it does. Romer was also behaving badly just as the government has been. It was sort of a mutually-destructive power struggle that, sadly, hurt the people of Honduras most of all by jeopardizing the integrity of the reforms.
Further, the ideological aspects ('free market zones' etc) distract from a more important idea – namely that cities can incubate better policies more safely, cheaply, and effectively than if reforms are tried first at the national level. Think Lean Startup for political reform.
The use of neighborhoods and municipalities as testbeds for reform is politically neutral... and it ought to stay that way, contrary to the wishes of some in this article!
Please consider visiting www.startupcities.org for a practical alternative to the 'charter cities' idea.