For me..
I view the Blue Pill representing those who are comfortable in answering all their questions by different set belief systems (both dogmatic beliefs and unquestioned ideologies, etc). They accept reality as it is imposed by external entities (religions, governments, social norm, etc).
The Red Pill for me represents that never-ending search for "truth" or not accepting any one's answer to the questions. A free-thinking individual who can accept to say, "I don't know" and then search for the answers himself. An individual who can see past the externally imposed reality and begin to realize that this is only a collectively accepted reality, and that it is not the end-all-be-all, etc.
Hope I communicated my thoughts clear, I can always expand and correct them if need be.