What is the main theme of the novel?

The Scarlet Letter is a Romantic indictment of the destructive qualities of society and the institutions it creates. It is also a passionate defense of Nature.
The behaviors that Arthur Dimmesdale and Hester Prynne display toward one another outside the judgmental realm of the colony are purely natural. What stands in the way of their fulfillment are the laws and mores of the Puritan society by which they have consented to live. Pearl, the product of their natural relationship, is, for most of the novel, too young to understand the culture that seeks to squelch her own natural passions. She was conceived in Nature and feels most at home there on purely unconscious and subconscious levels.
Hawthorne seemed to believe that humanity's natural condition was good: loving, generous, compassionate, and happy. What gets in the way and turns humanity to a darker condition are the institutions, primarily religious and legalistic, that confine and constrain, causing anger, pessimism, and the inevitable persecution of others. The natural world is the only place in the novel's settings in which any of the characters find a temporary respite from their unhappy lives.

One could specify several main themes to this story: sin, guilt, lust, and dishonesty come to mind. But I think a significant theme worth exploring is that of double standards of morality for men and women.
Hester Prynne is publicly shamed, made to wear a scarlet letter "A" on her clothing, for her "sin" of adultery. She bears a child (a daughter named Pearl), and this child is also shamed by the villagers, as she is seen as evidence of her mother's adultery. But Hester is proud and defiant, knowing she did not do anything wrong but only followed her heart. But during this period in history, women were considered the property of men, and their sexuality was subject to the strict puritanical values of the era. Oftentimes pregnancy was the source of shame and shunning for single women, and paternity could not be determined, so it fell upon women to bear their burden alone if men did not admit their involvement.
When it is discovered that Hester's lover and the father of her child is in fact a clergyman, the double standard of morality for men and women in this context is exposed. The hypocrisy of the church, which was the source of moral guidance for communities in Colonial America, is also exposed here. Hester may be guilty of sin, but she is being judged based upon the tenets of the church, and since it is a clergyman who is her lover, there is clearly a double standard of behavior and integrity that applies to men and women as well as to clergy and laypeople. Her lover is also guilty of this sin under the these standards. But the two are in love. Hawthorne's message on some level seems to be that love transcends social norms, and hypocrisy stands in the way of lovers who cannot be together because of social expectations.