To clear the air, there is certainly no reason to ban Vishwaroopam. In any sense, any form of creative act shouldn't be banned, especially in a democracy that values free speech.
And Vishwaroopam is just a film, no threat to Muslims – in India or anywhere.
Vishwanath and Nirupama played by Kamal Haasan and Pooja Kumar respectively are not so a happily married couple living in New York. Vishwanath teaches Kathak for a living while Nirupama has just completed her Phd in oncology.
With her boss, Deepak portrayed by Samrat Chakraborti hitting on her and the lack of love in her marriage; she wants a divorce from her husband.
Pooja ropes in a private detective to unearth an affair or a flaw in Vishwanath so that Nirupama can use it as grounds for divorce, but a sudden turn of events leads to his death and Vishwanath's real identity that he is a Muslim which leaves her stunned. Is Vishwanath a Hindu, or a Muslim terrorist? That's how the story moves forward.