How were non-muslims treated in the ottoman empire during the early modern period?

By the standards of the time, non-Muslims were treated reasonably well in the early modern period (1400s-1700s). They were not treated completely as equals, but were allowed to practice their faith and were ensured certain protections against gross discrimination and harm. 

They also had to pay different taxes, and were subject to a different court system for settling disputes. However they did not have to abide by all sharia-based law, and were allowed a greater level of social and political autonomy.

The answer is monsoons.