I am not sure what Jinnah said about it. But what I think about why a state should be secular is :

(Mentioning only few points)

1. Minorities (Non-muslims) are not getting their rights. Take an example of a pre-engineering students who are hafiz-e-Quran. They get some additional marks in their entry test score that help them to get admission in institute while hindus and christian students who have memorized Gita and Bible are not given any additional marks in entry test score. This a RELIGIOUS DISCRIMINATION.
(This still happens in NED engineering university Karachi)

2. Non-muslims are not eligible to become president or prime minister of a country. Why is it so ? If India where hindus are in majority, can have Muslim as head of the state then why not Pakistan ?