I do realise that muslims worry about the RSS and Bajrang Dal and so on. But muslim view of the BJP need not be at the same level. I know that the BJP leaders lost control of the mob in Ayodhya. Most Indians are sorry about that and have said so to their muslim friends many times.
I hope, you will think about the sequence of events - history, in other words, chronologically.
1) The 1920 Khilafat killings of Hindus has to be the first major "pogram" of the 20th century. Estimates vary but at least 20,000 - 40,000 Hindus were killed in Kerala and Bengal by returning Hajis upset over the abolition of Khilafa.
2) Despite the horrible experience of "Non-muslims" in the areas that became Pakistan,[At least 500,000 non-muslims killed, 29,000 Hindu Sikh women kidnapped and kept ] the "Sanghis" won no parliamentary seats or even MLA seats for many, many years. The Hindus wanted to settle down in peace with the muslims who stayed back in India. No "ethnic cleansing" was attempted.
3) After so many decades of "secularism" and Congress, Bollywood and "The Hindu" newspaper showing muslims in the best possible light, muslim militancy took an ugly turn, first in Kashmir and then spread to some Indian cities.
4) The ISI of Pakistan and LeT have been relentless in fanning militancy amongst Indian muslims. SIMI obliged them.
5) Even without the BJP in the south, nearly 8 years ago, a baazaar bomb in Coimbatore killed about 70 or so and maimed many more.