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.
The Handmaid's Tale by Margaret Atwood was published in 1985, and in some ways is similar in its vision to Orwell's 1984 in projecting a dystopian totalitarian future; given its probable date of composition, it seems likely that Atwood had Orwell's book in mind while writing.
There are several messages being conveyed by the novel. First, it is written from the perspective of a Canadian author looking with some distaste at the culture of the United States, especially at what seems from a Canadian perspective, to be the disconcerting powerful influence of right-wing religious extremists, leading to racial discrimination, gender inequality, and xenophobia. Just as in the early nineteenth century, Canada provided a refuge for escaping black slaves, and in the 1960s a refuge for young men avoiding being drafted to serve in the Vietnam war, so in Atwood's novel it become a refuge for women escaping gender oppression.
The main message of the novel is one which supports gender equality and personal liberty against the forces of ignorance and prejudice. It especially argues that the two are linked. Prejudice and inequality spring from ignorance and restricting information and freedom of speech are the marks of a totalitarian government. Literature, and especially the classics, are especially important for the way they develop and free the human mind.
The Handmaid's Tale certainly fall within the category of being a dystopian novel, and as such one of the central messages of the novel addresses the role of government in limiting the free will of the people. Throughout the novel, Atwood provides a multitude of examples of characters who protest, embrace, or merely put up with the harsh system of the new government of Gilead.
Atwood utilizes the over-zealous structure of Gilead with its commanders and rigid laws concerning both men and women's roles in society to force the reader to analyze how society categorizes people based on gender and at the same time, how people of both genders either accept or deny those roles. Gilead is a hyperbole for everything that is wrong with gender roles, and Atwood exploits it to force the reader to question the currently accepted definitions as well.