Of The Handmaid's Tale, Margaret Atwood once said,
"This is a book about what happens when certain casually held attitudes about women are taken to their logical conclusions. For example, I explore a number of conservative opinions still held by many—such as a woman's place is in the home. And also certain feminist pronouncements—women prefer the company of other women, for example. Take these beliefs to their logical ends and see what happens [....] I decided to take these positions and dramatize them, carry them to their furthest logical conclusions."
Therefore, I think it is reasonable to surmise that one major theme of the book has to do with the dangers of extremism, no matter what the kind. This is not to say that either religion or feminism, for example, is extremist by nature, but part of Atwood's point seems to be that any position can be carried to extremist levels.
Furthermore, it seems that extremism can become even more dangerous, when coupled with gender roles. When gender roles are as rigidly defined as they are in Gilead, no one is happy; no one is really free (another theme). Even Offred's commander, arguably the character with the most power and personal freedom, is unhappy. He routinely breaks the rules he helped to create by having private meetings with Offred, playing Scrabble with her, and then taking her to Jezebel's. If he were happy with his role and the rules, he wouldn't need to step out of that role and break those rules.