As a general rule, stories need conflict; there must be something that the protagonist wants to do and something that keeps him from doing it. Dystopias provide a more fertile ground for conflict than utopias. It's just that simple.
Also, when the theme of a story involves society, it's almost always necessary to show a malfunctioning society in which to express thematic conflict. E.g., it would have been hard for Rand to have done what she did in Atlas had she set her story in something like Galt's Gulch. Similarly, Atwood's story (I haven't seen the dramatizations) needs its dystopia in order to most effectively make her points.
I note that Atwood was hardly the first to see the possibility of a Christian dictatorships in America. E.g., Heinlein did it in 1940, in "If This Goes On".