Why was Caravaggio's work sometimes rejected?

Answer 1

Caravaggio was controversial because he often depicted religious figures in a way that the Church disagreed with. For example, in this painting of The Death of the Virgin, it is said that he based his depiction of the virgin off of a dead prostitute that he pulled from the river. The point being that he depicted saints and religious figures as normal looking humans rather than idealizing them.

Answer 2

It was too brutally naturalistic.