Drug abuse
The first and most important theme of the book is the issue of drug abuse. The characters in the novel quickly decide that the public, government issued information about drugs is wrong and political. But, that leaves them prone to do "drugs" in general. The problem is that, although the hippy drugs are non-addictive chemically speaking (LSD is the main one in this novel, but also marijuana and other hallucinogens), they are often mixed in with other drugs that are way more addictive and dangerous. So the characters are left with wrong ideas about what drugs are and what they do to them.
Naivete versus wisdom
In the book, the characters are constantly discovering that their expectations were wrong. That means that they are naive, because they assume things are safe when they aren't. Eventually, they end up in the wrong side of the criminal underground in a country they don't live in, where they don't speak the language. How different is Mexican crime life from a happy healthy life in San Francisco? That is how wrong their naive perception was. But in the end, they have stories about how they learned these lessons.
The hippy generation
A bunch of stoner hippies appear in this book. They are life-lovers, and their penchant for drug usage is primarily an attempt to understand the world and life in a broader point of view, but ultimately, that leads to the problems this book describes. The hippy generation was an important phenomenon, but drugs cannot solve life's problems. By conflating drug experiences for religious enlightenment, they accidentally behave in a foolish way, and they run the serious risk of addicting themselves to different kinds of drugs. These things all add up to one picture: The archetypal hippy. In other words, the book offers a snapshot of what it felt like to be there during those times.
