The roots of Colombia's conflict go all the way back to the colonial era. Add in the production of cocaine, modern ideology, the various ethnic groups living in the country and its rugged geography, and you have recipe for long lasting violence.
The Spanish empire was an extractive one - that is, it sought to take as much wealth as it could from its colonies to enrich Iberia. The indigenous were worked in the mines and plantation until they died in great numbers, after which African slaves were brought in. Conquistadors set off on expeditions of exploration and conquest and were rewarded with land. These developed into huge estates and a system known as encomienda - in which native inhabitants were obliged to give their labour to the local Spanish landlord. These landlords oversaw the stripping of their country's wealth but lived comfortable lives. Little attempt was made to build industry as the colonies were not meant to be developed and self-sustaining places. Land therefore became the only source of wealth and social status, and it was concentrated in a very few people's hands.
Colombia, and most of the rest of Latin America gained independence when Spain was invaded by Napoleon. Across the region however, it was not an uprising of disgruntled and exploited peasants. Instead it was the white landowning Criollo class who launched the independence campaigns. They were still essentially Spanish people, but they had been born into their new world encomienda estates. Once they had succeeded, the question of what their new countries would look like came to the fore. Two main camps emerged and again, this was true of both Colombia and the region as a whole.
On the one hand you had conservatives who wanted a new homegrown monarchy to rule (or one imported from the nobility of Europe) and for the Catholic church to play a large part in structuring society. On the other, you had the liberals. These people were influenced by the enlightenment ideas of Europe (and France in particular). They wanted to form republics ruled by enlightened despots, and leaned towards written constitutions and more secular societies. They were the progressives of their time, but they were not truly revolutionary. They were still rich, upper class people who were happy with the social order of things, even if they wanted political change. Most had no qualms with the fact that most of the population lived in poverty, and had no intention of handing out their land to those in need.
Now these two factions would in places resort to open warfare. In Nicaragua for example, Leon was the city of liberals while Granada was the city of conservatives, and the two cities spent much of the 1840s and 50s locked in civil war. Colombia suffered particularly badly from this phenomenon.
While it is well known that Colombia has had a conflicted second half to the 20th century, in truth that conflict grew out of the earlier liberals vs conservative conflict. It would be more accurate to say that it has been in conflict since independence. It was involved in the break up of Gran Colombia (a confederation of Colombia, Venezuela and Ecuador), it suffered a two year civil war in 1860, and then another (known as the Thousand Days' War) in 1899. Between and after these conflicts it was involved in a brief war with Peru, had Panama taken off it by the United States and the liberal/conservative conflict would flare up regularly even when full blown civil war was not taking place. Things boiled over again in 1948 when a liberal politician was assassinated. The capital - Bogota - erupted into rioting which destroyed much of the city centre. What followed was a ten year period called 'The Violence' which killed hundreds of thousands of people.
By this point the world had entered the cold war and the age of ideology. Until now, radical rural peasants had generally supported the liberal party even though the party was still one of the upper class. Now however, more radical ideas started to flourish. They started seriously questioning why they couldn't own land, and why their lives were a struggle for survival when the ruling class lived so well. The FARC was founded after a group of peasants occupied a large farm, and were eventually beaten back by the army. They took to the hills vowing to create a socialist society that looked out for the interests of the poor and which would redistribute land. They were inspired by Castro's successful example in Cuba (successful in terms of obtaining power - the success of his regime is a different debate). Soon after other groups started to form. M-19 was founded by radical students and academics for example.
The same thing happened across Latin America with left-wing rebels appearing in almost every country. Because this is Colombia however (the land of magic realism), things got a lot more complicated than a simple government vs rebels conflict. The land-owning classes started to form private militias which they used to protect their interests, indigenous groups formed self-defence forces to keep the warring factions out of their lands and of course, the cartels appeared.
Coca and cocaine were the accelerant which really confused the situation. There was a general lawlessness in the country due to the civil war. FARC controlled much of Colombia (at one point almost a third of the nation), the landowner's paramilitaries also controlled parts. Vast swathes of the country were out of the state's control, and so enterprising 'businessmen' like Escobar were able to exploit this space to build their own cocaine empires. Soon, the left-wing rebels got in on the act as they needed to fund their war, and the right-wing militias as well as their rich bosses were not against new ways to solidify their money and power. Soon the cartels controlled parts of the cities and owned coca fields of their own in the country, and so even more of Colombia slipped from the government's grasp.
At this point things were a real mess. While the FARC and the other left-wing groups still shouted loudly about their intention to make the lives of ordinary people better, by now they had become hopelessly corrupted by the cocaine trade and the harsh realities of war. They would turn up at a village and demand assistance from the helpless locals. The government or the paramilitaries would turn up a few days latter and kill those who had assisted. The same thing would happen in reverse, so that most poor farmers feared the FARC as much as the militias despite their interests technically aligning. To make things even murkier, the lines between the groups were not blured. Militias would work with cartels, who would also work with left-wing groups if profit could be made from it. The government/army/police was riddled with corruption so individuals would would with everyone except the rebels. There are proven cases of militias working with government officials despite their extra-judicial actions and involvement in cocaine. It became difficult to tell sometimes who was a rebel, who was a drug lord, who was a paramilitary and who was working for the state.
That's a brief overview of things, and of course there is a lot more too it. I can't really go further and explain how things slowly started to settle down a bit as it would violate the 20 year rule.
Sources:
Masters degree in Latin American Studies
Edwin, Williamson - The Penguin History of Latin America
Rosa, Michael - Colombia, A Concise Contemporary History