During the early 1980’s there was a lot of tension between the Muslims and Hindus in India. This tension caused them to divide into two, most of the Hindus staying in India, and the majority of Muslims went to Pakistan. Obviously over time both cultures have reached other areas, but this was where they first went with the division. To put it bluntly, the Hindus believed in one thing, which clashed with the Muslims who believed in something different.
This tension caused Muslims to be discouraged from marrying a Hindu, which Khan and Mandira did. That’s why in the movie Khan’s brother was against seeing him, for he had ‘betrayed’ his religion.
Source: http://www.conflict-prevention.net/page.php?id=45&formid=72&action=show&articleid=23
My Name is Khan 