Setting asside from his scandalous private life and his white-hot temper, Caravaggio's work might well have been sweeping enough in it's naturalness and "newness" to have avoided much of the controversy and criticism that dogged his every artistic effort, except for the fact that he often worked for the church. Then, as now, the church was a temple of conservative thought, especially during the counter-reformation. This included doctrine and dogma of course but also matters of art as well.
About 1597, Caravaggio received a commission for several religious paintings to decorate the Contarelli Chapel. Among these were The Martyrdom of St Mathew, The conversion of St. Paul, and most controversial of all, the final one, The Death of the Virgin done completed in 1506. Caravaggio's brand of "naturalness" demanded the use of unsanitized, peasant, dirt-on-their-feet models, in no way resembling the idealized firgures of Raphael or Caravaggio's main rival at the time, Annibale Carracci. In The Death of the Virgin, the figure of the Virgin was derived from the drowned body of a prostitute (for that bonafide "dead" look, no doubt). Predictably, the word "blasphemy" came to mind as word of this sacrilege reach the ears of most church figures.