1. Rightly or wrongly many Hindus see Sikhs as a part of Hinduism. Since the religion originated in Indian subcontinent they don't see it as an outside religion. Many Hindus and Sikhs go to each other's places of worship, intermarry, jointly celebrate festivals. This is what many believe, so a Sikh PM is more acceptable in this democracy. Sikhs are also more trusted by the Hindus. Muslims can't enjoy the same privilege because of historical reasons, latest being 1947 partition.
2. Manmohan wasn't a politician, he was an economist and RBI governor. Congress brought from outside and made him finance minster during our economic (BOP) crisis in 1992, then he became a puppet PM. He never had an independent voice and was the mask, real rulers were Sonia Gandhi and Rahul. Such a situation is possible for Muslims, example Abdul Kalam a scientist was made President by BJP even when he had no link to politics. In the future an outstanding achiever like Manmohan, Kalam can be brought from outside and made puppet PM.
Our democracy is flawed, it is tough to be mass leader for Muslims when 85% are non-Muslims. There have been some Muslim chief ministers but PM is tough. We always had the Nehru dynasty and their sycophants in that job, recent times BJP has put candidates like Vajpayi and Modi.