From Cuba to Chile, it seems like most Latin American countries have been ruled at some point by a caudillo, like Juan Manuel de Rosas in Argentina. Why were those countries so vulnerable to being taken over by caudillos?
For starters, it is important to understand that the historical institutions that developed in Latin-America through the 1800's vary a lot in their solidity and ideological background. There is not such a thing as a "Common Latin American Political Culture" as an Argentinean will definitely see himself as part of a whole different culture from a Colombian, or a Chilean from a Peruvian.
In my answer I will concentrate on Spain and Chile which are the countries I know best.
For instance, Chile had a constitution from 1833, albeit a very conservative one made by Diego Portales, that lasted for 95 years. That longevity and stability is unique in Latin America. Around the last half of the 1800's Peru and Bolivia had suffered from several coups that weakened their governments and damaged their possibilities to effectively wage war against Chile in 1879-84. Chile even managed to hold elections during that same period, which tells a lot about the political culture/stability compared to its neighbors. (1)
Now, the Caudillo "culture" or paradigm of government has its roots in the fractional regionalist nationalism that has been a part of Spain for ages. After Fernando the 7th came back from France in 1813/14 there followed a period of horrendous political instability, civil wars (carlist wars) and regular "pronunciamientos" by military leaders around the country. A "pronunciamiento" is basically a threat from a military unit to revolt if certain changes in government are not implemented, although not "coup de etat" per se, they still have that combination of "strong man" leadership and will to use power in order to get changes implemented. The "caudillismo" comes from Spain. Given the problems caused by local nationalism in spain in allowing a government to maintain a strong presence and create an image of a "nation" above the local regionalism, Given the resiliance of certain parts of the population in spain against "liberal" reforms it created an unstable political atmosphere in the country for a long time. Such was the national trauma that the word republic became associated with chaos. This entire process lead in the end to the “Primo de Rivera” dictatorship and the so called regenerationists, an intellectual group trying to find a way to fix Spain's problems. You could say that General Franco was his spiritual successor, not ideological (that point can be discussed) How does that relate to south america?
After the independence wars during the first decades of the 1800's it was extensively debated about what kind of government the different countries should have. Off course, those discussions found place among the (mainly) conservative catholic aristocracy of south american countries, the "pueblo" or people did not have a say on this. Neither had their any interest in that. South American liberation was a revolution by the elites. The great general San Martin even theorized and flirted with the idea of inviting a european monarch to La Plata. In Chile, the liberator Bernardo O'higgins got the title of "Supreme Director" by the national assembly or "junta" of aristocrats, he reigned for a good while until again, the same aristocrats ousted him, claiming him to be “a dictator” and abusing his power (unfounded claims). Throughout the liberation wars, actually having anything close to an atmosphere of collaboration was impossible and "strong men" would usually take power just because the alternative was banditry and pillage. Here it is important to understand that the South American ex-colonies and the aristocracy were terrified by what could happen if “jacobites” or freemasons came to power, they were seen as “godless dogs” and Roberspierre type tyrants. they feared what happened in Haiti and the slave revolts there. Hence, whenever a populist came to power, the military (which the aristocracy dominated) would revolt and put one of their own in power. And thus the cycle continued intermittently.
Now Chile has a different history given its unique culture and homogenous population. Which in my opinion is the main cause for the country's relative stability. It all started with the 1833 constitution and Diego Portales. Several military victories over the neighbors also consolidated the national identity and the state's legitimacy which in turn increased stability. That does not mean that the country did not have troubles. In 1891 there was a short Civil War that ousted the president and increased congress power. But that is another story.
Hopefully I have managed to answer partially your question.
Sources: Stanley Payne, A history of Spain. The Franco Regime. Fascism in Spain.
Gonzalo Vial Correa: Chile, Cinco Siglos de Historia
William Sater: Andean tragedy, fighting the war of the Pacific 1879-1884