Your question stems from a common misconception about the cultural, social, and political realities in colonial Spanish America. It is easy to assume that the Spanish colonies were united, so when they had an opportunity/reason to gain independence, all they needed to do was declare/fight for it (a la the United States). However, a unified, coherent society simply did not exist anywhere in Spanish America. Instead, we need to think about pre-independence Latin American colonies as self-interested “cultural islands” separated by huge gulfs of frontier space. We can still see the legacy of this fragmentation today by looking at a population distribution map of South America. Most of the people back then (and today) were concentrated around Spanish metropolises scattered throughout the colonies. These different localities had independent interests from their neighbors, retained unique cultural heritages that created “us” and “them” mentalities, and faced virtual isolation from nearby provinces and far away colonies alike.

Their separation and isolation was further sharpened when we think about the geography involved. Spanish America stretched from southern Canada to the tip of Tierra del Fuego, a distance of roughly 8,000 miles (about 13,000 kilometers). This territory also included some of the longest mountain ranges (Rockies, Andes, Sierra Madres) and river systems (Mississippi, Amazon, Paraná/Uruguay river basins [depending where the borders were drawn, which changed over time]) in the world. Also included are deserts, rainforests, highlands, and plains and almost every type of climate region present on Earth. Scattered throughout this territory were thousands, perhaps millions of people with rich histories and cultures all their own. Some were slowly incorporated into the colonies while many others were openly hostile to colonists, making traveling through the colonies dangerous. The Spanish Empire was stunningly immense, diverse, and fragmented.

Scattered in this massive space were small Spanish outposts that over the course of the 16th, 17th, and 18th centuries grew into cities and towns. Spanish control spread over the land at varying rates that changed over time and differed geographically and economically. Initially, the empire was organized as an extractive empire whose wealth was sent back to Europe. Under this system, infrastructure was only developed to support extraction, which kept Spanish cities isolated. Shipping silver from Potosí for example meant sending it to Lima, then to present-day Panama, where it was eventually sent back to Spain in convoys. Once again, it’s easy to think to our modern selves that this system was illogical and cumbersome, but at the time, it was cutting edge, drew on the dominant economic theory of the day (mercantilism), and propelled Spain to be a competitive world power for centuries. Yet the lack of investment in the peripheries hurt economic development in the long run. The colonies were isolated and vulnerable to attack from outsiders. A vast majority of citizens lived in abject poverty with little stake in political or economic systems (although the same was true of most people in the world at the time). Spain was in the process of modernizing its empire at the end of the 18th century to make it more competitive with up-and-coming nations like Britain. Spanish rulers redrew borders, introduced trade reforms, and drastically increased defense spending. Many in the empire expected even more drastic change in the coming years, but Napoleon intervened and inadvertently launched Latin America on an entirely different trajectory.

Napoleon put his brother on the throne, who virtually no Spaniard viewed as the legitimate ruler. In the absence of a king in traditional Spanish law, power reverted back to the people to rule until a rightful king was found. Without realizing it, Napoleon had untied the monarchy, the only thing that held this vast empire together at all. Immediately the viceroyalties, intendencias, and cities on both sides of the Atlantic began bickering among themselves about who should rule what in the place of the king. They all tried to assert their own interests, many of which had been repressed under the old Spanish colonial system. Lacking any unity and separated by the vast spaces and geographies detailed above, the colonies were swept into a period of power negotiation during which new forms of rule were tested for the first time (not unlike the Articles of Confederation period in the United States where a new form of government was tried and later discarded). This was led by famous rulers like Bolívar. Unfortunately, these first attempts quickly fell apart into chaos and civil war because there was so little to tie these new territories together. Bolívar supposedly said something to the effect of “those who participated in the revolution have plowed the sea.” Over the course of the subsequent civil wars, the nations that we see today began to emerge. This was a gradual process which was not fully completed until the late 1800s when smaller, stabler nation-states finally demonstrated a degree of cohesion and strength.

As a case study, let’s look at the Río de la Plata Viceroyalty, created in 1776. On the surface it looks coherent and unified. In many ways, it was the most “United States-esque” with small indigenous populations, plenty of agricultural space, room to grow on the frontiers to both the northeast and the south, relatively easy access to trade with Europe, and immigrants pouring in. It stretched from Peru to Patagonia and contained vast mineral and agricultural wealth. Following Napoleon’s invasion, Buenos Aires tried to assert itself over the rest of the viceroyalty, claiming that power had reverted back to them. Buenos Aires assumed that it would maintain its position of authority over all of “its” viceroyalty, but very few of the provinces willingly recognized the city’s supremacy. Paraguay and Alto Peru (the area around Potosí) refused to recognize Buenos Aires as their legitimate rulers and broke away from the United Provinces of South America. Buenos Aires sent armies to seize “their” renegade provinces, but in all cases, they were defeated. Meanwhile Chile, though part of Peru, was completely cut off from both Buenos Aires and Peru by the Andes and the Atacama desert, allowing them to virtually rule themselves in their own interests.

In the Banda Oriental (what would one day become Uruguay), resistance to Buenos Aires motivated José Artigas to propose a new league of power against Buenos Aires, which was then crushed by Spain’s long-time rival Portugal, who looked to assert themselves in the Banda Oriental. After all, the Río de la Plata had been a long time flashpoint between the Spanish and the Portuguese empires. The Portuguese saw an opportunity to tap into the agricultural wealth and began pushing their claims once again in the midst of the chaos. They threw out Artigas, which then sparked a war between Portugal and Buenos Aires, which would eventually lead to the creation of Uruguay following even more chaos and civil war.

So that was an incredibly simplified rundown of the basic reasons why Latin America fragmented into many countries. That summary only concerned the Southern Cone. I barely touched on northern South America, Central America, or Mexico. In all cases, Napoleon’s actions forced local, introspective, self-interested “islands” of culture, through political discourses and open combat, to figure out how to be independent nations. This took a long time, often decades or more. No unified nation emerged because no unified set of colonies ever existed in the first place. The political, cultural, geographic, and economic differences between localities were too much to overcome.

Well, not all Latin American countries were (former) colonies of Spain, nor did they all achieve independence at the same time. In fact, there are still "neo" colonies in the Latin America/Caribbean region. For example, Haiti -- at the time of its independence, a French colony -- was freed via revolution in the early 1800s. On the very same island, the Dominican Republic (a Spanish colony) didn't gain full independence until the mid-1800s and even then, was still subject to meddling from Spain and even suffered U.S. occupation during the early 1900s. There are still de facto colonies in Latin American and the Caribbean -- most of which, aren't in fact Spanish -- including Guadeloupe, Martinique, and French Guyana (French overseas "departments"), to name a few examples.

Your reference to Bolivar is a good start to an answer for this question. While there were different movements throughout Latin America to create a single state, none have been successful. The reasons behind this are numerous, however for the sake of this conversation we can dwindle it down to a few key points.

Geographical diversity: Latin America, reaching from Mexico down to the southern cone of Argentina and from Cuba across the andes is an incredibly large place. Total land mass is over 8 million square miles (http://wdi.worldbank.org/table/3.1). This creates a difficulty in a centralized governance even with the technological capabilities of today. The differences in geological formations in different areas of Latin America lead to a diversity of population. A simple example is that the people of the Peruvian Andes would have a difficult time rectifying common national needs with those in the low lying areas in Buenos Aires. This type of dissociation made it difficult for those looking to create a unified state. While we do see success in creating a regional "Bolivarian" state and identity it can be argued this was in spite of this obstacle and any extension would run into our issue of Geographical diversity.

Sorry coming back to this after work