The pills represent a choice we have to make between accepting the truth of reality (red pill), which could be harsh and difficult, and maintaining our blissful ignorance of the world (blue pill), which is way more comfortable.  

"You take the blue pill, the story ends. You wake up in  your bed and believe whatever you want to believe. You take the red  pill, you stay in wonderland, and I show you how deep the rabbit hole  goes."―Morpheus to Neo

In the context of the Matrix, a person who picks the red pill will become aware of the Matrix itself and what the machines are doing to them. Someone who takes the blue pill gets to continue living in ignorance, none the wiser of what they are being used for. 

If we extend this to a philosophical standpoint, we are faced with the deeper meaning of the choice. Are we ok with living an ignorant life as long as we are happy? Or will we want to search and find the Truth even if it will be a difficult truth to embrace.