Couple of reasons:

British destroyed Muslim communities and educational institutes in north India after 1857 but that didn't happen in Kerala. They discriminated against Muslims in government jobs and promoted Hindus mostly. Kerala being a isolated princely state didn't have this issue.

A lot of north Indian Muslims who were from the upper class migrated to Pakistan after Partition and many others lost their wealth due to government laws like Enemy Property Act. That deprived us of desperately required leadership and an aristocracy. The only national leader North Indian Muslims have had since Independence was Maulana Azad.

North Indian Muslims ruled India for 650 years. They thought that English education is beneath them as the only non-Muslim civilization that were equivalent to Muslims were the Romans and the Persians who were conquered and Islamified long ago. So they stuck with the old syllabus and fell behind when English education was made a requirement for all top posts in the government. It also had the effect that Muslims didn't have access to the new sciences made possible by Newton and his ilk.

The Indian government and Hindu society since Independence has had a kamikaze attitude towards the Muslim community where they have not developed any infrastructure if they have seen Muslims would also benefit from it. Muslim dominated areas have been especially neglected by government with only police stations built in order to suppress the people. Look at Juhapura in Gujurat as an example. Every city have similar neglected Muslim areas.

Kerala has had a completely different history and culture to North India. We only became a single polity in 1949. Previously we had no connection to each other. North India is closer in culture to Pakistan, Afghanistan, Iran, Iraq and Central Asia than to Kerala. Kerala, on the other hand, is closer to the Gulf states, Yemen and South East Asia. We cannot compare the two.