And
why not?
What easier way is there of relating deep philosophical concepts to the masses than something deeply ingrained into popular culture?
The average person would probably think you were insane if you tried to explain the "brain in a jar" theory. But most people understood the visual metaphors in Neo's removal from the egg.
Try to explain the concepts of subjectivity given in David Lewis' Mad pain and Martian pain to the average Joe and you'll probably be greeted with a blank stare. But using examples like in How does the Matrix know what blue is? could clarify the matter greatly.
In short, there is no shame in using a well-known reference to explain philosophy to outsiders. The Matrix has been overanalyzed to death, yes, but if you use it as a reference and visual aid rather than discussing how Neo is Christ, you can probably get away with it.
Of course, if your conversation partner has never seen The Matrix, then you're obviously forced to use other references to help this person understand. But such is the way of life.