The Matrix is an intellectual and philisophical metaphor for life. Addressing questions and ideas which reach deep into religious concepts such as 'what is the soul?' and 'do we truly have free will?'. I find it intriguing considering this weeks Torah portion contains the phrase 'I place before you a blessing and a curse, life and death, choose life...'. Thus the concept of Free Will is expressed in clear terms. But the matrix views angels and dark forces as sub-programs in the matrix, and the question of free will is a bit more complex. The pseudo-religious messianic overtones are glaring, the Neo is 'The One' who can bring down the machines and restore 'Zion'.
I don't know the political or other stances of the writers and directors. I just think the concept was very interesting.