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The question is not whether or not he was a protestant or catholic. He was an Italian living in the 17th century - almost guaranteed to be Catholic. However, although he painted for a Cardinal of the Catholic church, he developed what was considered a secular style by painting saints in an unidealized manner, as ordinary people in a very realistic manner. This style was quite controversial.

The outstanding characteristic of Caravaggio's painting style was the use of tenebrism - the use of light and shadow to increase drama and emotional tension when viewing the painting. The style is quite recognizable - the paintings look almost as if a spotlight is shining on certain aspects of a grouping while throwing other parts of the grouping into shadow. This style is considered a hallmark of the Baroque era of painting.

Caravaggio painted Catholic themes very often in a controversial manner mixing in his personal lifestyle with subtle suggestions of (homo)sexuality and temptation. There are many controversial overtones in his paintings that some consider teasing and toying with the church (Catholic), the primary patron of art at the time. He was always getting into trouble and having to leave town. He ended up killing someone but died of an illness while on the run. He used the light/shadow approach known as chiaroscuro and his point of view placed the viewer in the scene at ground level. The attitudes in his figures also reflected reality and common man rather than classical ideals.