In your brain is are chemicals called neurotransmitters. These are transferred between the cells (called neurons) of your brain to communicate messages. There are two key neurotransmitters that caffeine affects. The first of these is called dopamine. Dopamine is released into your brain to communicate the feeling of pleasure and it is needed for motor functions. Essentially, it reinforces us to continue doing whatever we are doing. When dopamine is released, it floats around in the space between neurons (called synapses) until it locks into dopamine receptors of neurons. When this chemical latches to a receptor, we get a nice happy feeling.
The other neurotransmitter affected by caffeine is adenosine. This neat little brain chemical is responsible for helping us sleep. When adeonsine is released into the brain, it binds to adenosine receptors, much like dopamine. When this neurotransmitter finds a neuron slot to bind to, it makes us feel drowsy by slowing that neuron's activity. It just so happens that caffeine looks like adenosine to the brain, so it takes adenosine's seat in the neuron by binding to its receptor instead. Caffeine doesn't slow down the neuron so the effects of the sleep-inducing adenosine are staved off - if only temporarily.
So you can see where one might get the idea that caffeine programs your brain. Personally, I'd call it hacking.