I would like to point out here that it has been seen according to research that many people in India do not differentiate the Mongol and Mughal regins and accordingly, on both sides, associate the Mughals as the symbol of power of the Muslims in the region. The Mughals also get blamed for the tactics of the Mongol raids, in the immediate aftermath of Genghis Khan, to the Mughals and thus the Muslims. Here are two examples:
http://www.psr.jku.at/psr2005/14_02Sen.pdf
Culture, Social Representations, and Peacemaking: A Symbolic Theory of History and Identity - Springer
Historically these eras and civilisations are very different, the Mughals were a Turkic-Perisan influenced peoples, that had inherited Mongol blood but not much of her culture. Moving forward, the Muslim reign on South Asia comes under first the raids from the land of what is now Afghanistan, that again has nothing to do with religion, it has to do with the history and culture of the region, this practice was carried well into the 18th centuary. Here is what comes up, once the Muslims were populated here, it was often seen that the raiders were 'softer' on the Muslims, however, this has nothing to do with any planning or any sinisterisation of the whole plot. It was an occurance of History that was never carried with certanity and the myth of the Muslim being the 'outsider' to the region was created over at these instances this is especially true as the Marhata's and later the Ranjit Singh's kingdoms begin to decline. This happens because of something 'Anchorage' according to Social Representations theory
An Error Occurred Setting Your User Cookie I believe this article explains this. Not sure if you can access it, sorry. Let me see another one if you want.
Now then, come again to the later times, the partition, cements this feeling in both societies and history is read without context to paint the light of giving weightage to either this side or that one. Conservative rightists over here tell us tales of the Sikh conquest and Sikhs desecrating our Mosques. People on your side tell you about Muslims raping and converting as they go. These are out of context, and misplaced because most people do not appreciate the feel and life of the era. (Cominng to the Sikhs, the Mughal-Sikh dynamics were again political, not religious, Ranjit Singh had Muslim generals, the Muhgals employed a Hindu Army.)
I hope this can shed some light.