Domestic causes of the coup that are relevant to the international response: Zelaya's populism, Zelaya joining ALBA, Chavez.
This event is included because it shows right from the get-go that this new military government was a human rights violator - which, if human rights were a top priority in U.S. foreign policy, should have led to the U.S. suspending Millennium Challenge Corporation Aid, not recognizing Lobo's election, etc.
Most commentators seem to think the only reason this was able to happen was because the U.S. did not stop it. Given the amount of influence the U.S. has had over Honduras historically (it was the original banana republic, after all) and still has, this makes sense. Another case (like Operation Condor/Pinochet's Chile in the 1970's) where mixed signals from the U.S. government allowed a human rights-violating government to continue violating human rights.
At this point, Secretary of State Hillary Clinton had already decided that the Zelaya question was "moot."
The U.S. had recognized his election as legitimate months prior.
This represents the "swift, united action" that many commentators praised the international community for, even though it did not succeed.
The U.S. did not take part in this.
The U.S. agreed to this.
This shows that there was no question to the rest of the world that the government was perpetuating human rights violations.
Notably, it was Obama that said this, not Hillary Clinton. This was immediately after the coup and represents the administration's view before it was pressured by domestic forces.
This is an important event that we only know of thanks to Wikileaks. For months afterwards (until, arguably, it was too late), the State Department declined to act in several ways (cutting off all aid, such as MCC aid) because officials claimed they were trying to distinguish whether the coup was a "military" coup as opposed to... something else. Not only had that distinction not been made before, the "Open and Shut" cable shows that Ambassador Llorens believed from the start that the coup was illegal and constituted a military coup. There is some plausibility that the State Department did genuinely struggle to make a distinction between the Honduras coup and more traditional military coups because it was unique in many ways (the military was acting on behalf of the Supreme Court, and instituted a civilian interim president), but it seems more likely that they avoided the label "military coup" because political pressure or strategic interest made them not want to cut all aid or refuse to acknowledge Lobo's presidency.
Here is where it gets confusing. The State Department cuts off all non-humanitarian aid, in effect doing what would have been required of them had they labeled the coup as a military coup. Why drag their feet for so long, then? What reason could there have been for them to want to not label the coup as a military coup, yet still cut off aid? The most plausible explanation is that the U.S. preferred for Zelaya not to come back, so they did what was expected of them while still leaving the window open to later recognize Lobo as legitimate. In effect, they participated in the human rights regime while still having Zelaya out. Note that they resume aid several months later.
This is a turning point in the U.S. response to the coup in that domestic forces (Republican senators) start pressuring the Obama administration to keep Zelaya out. One month later, the U.S. recognizes the election as legitimate.
This comes after the Republican delegation goes to Honduras, the Senate blocks two Latin America appointments, and the Obama administration comes under pressure from Florida representatives.
Aid was only suspended from September 2009 to March 2010 - I would have to compare this with other cases (in Africa, most likely) to see exactly how it compares, but it seems so short and superficial that it was probably more to save face than to try to achieve an outcome or actually support human rights.