This is not a religious conflict, but a colonial one. Israel was set up by foreign people against the will of the Arab natives of the territory. That is the heart of the question. Religion complicates it all, but it is not the main issue here. Arab resistance against the colonialist regime is weak compared to Israel's might, hence the difference in prisoners number. It has nothing to do with their worth.
About 2,000 demonstrators protest 'occupation policy and fascist settlers' in Nazareth (Haaretz)
from the article: 'Shin Bet tortures prisoners and denies access to lawyers'