Many have claimed this an affront to organized religion or religious zealotry, but I'm not convinced. The Enterprise faces a society of people being controlled by a being called Landru. The people go about their lives in complete peace and tranquility, but at the loss of their individuality. They walk around murmuring greetings and well wishes, speaking of the unity of the "body" and the greatness of "Landru."
I believe, however, this religious interpretation falls apart when we learn the true nature of Landru: that he was a man who lived 6,000 years ago and upon his death programmed a machine to help his society maintain peace. In the light of this I think the familiar critique appropriate: be careful what you wish for. The hopes of society for attainment of any pure ideal that does not allow for the free choice of the individual is one that will come at dire costs.
The civilization we see depicted in this episode plays more as a warning for those who are proponents of such extreme ideals (potentially religion, but not specifically). I feel that this message may be a bit muddled in its final presentation, and an exploration of further themes or drama may have been wise. You see, nothing particularly dramatic or interesting develops of our characters or the guest cast introduced. The entire payoff of the show banks on the stressfulness of the issue at hand.
I will admit being quite amused at McCoy's trance when he is "absorbed" into the control of Landru. I can't for the life of me figure out if this amusement was intentional or not. Either way, the episode flirts with interesting ideas, but never puts our characters at enough risk or ties them to the outcome with enough sincerity to warrant severe reaction or dedicated interest.