Paolo Veronese, Feast in the House of Levi (formerly The Last Supper), 1573
I've always found it odd that the Inquisition went after Veronese, a very technically brilliant artist, but not perhaps the most thoughtful. He got dragged before the Tribunal over this painting, which the Inquisitors considered far too light hearted for a Last Supper. They even threatened Veronese with more serious charges of heresy. He was ordered to change the painting in 3 months. Instead, Veronese changed a few details and figures here and there and changed the title. No more was said and the matter ended.
And yet, the Inquisition never touched Caravaggio, a hustler, a thug, and a murderer from the Roman streets who brought that experience into his religious work. Some people still find his religious work to be deeply unsettling, especially a painting like The Death of the Virgin showing not some glorious Assumption or Dormition, but a quite dead corpse laid out on a plank surrounded by grieving Apostles.
Caravaggio, Death of the Virgin Mary, 1606
The public was outraged by this painting. Church authorities obliged the patron of the work, Laerzio Alberti, to remove it from the altar of a chapel in Santa Maria della Scala in Rome and to replace it with a less disturbing work by another artist, Carlo Saraceni. This is the painting that stands on the same altar today.
And yet, for all the fury over Caravaggio's work, he never faced any Church tribunal. When he did finally face a magistrate, it was not over any charges of heresy, but to answer for the murder of Ranuccio Tommasoni.
I've always found it curious that whenever Caravaggio paints some nude Roman street boy as "John the Baptist" (in this case, his auburn haired model, apprentice, servant, and probable lover, Francesco "Cecco" Boneri), everyone starts speculating about his sexuality. What's to speculate about? Sure the written testimony says that Caravaggio had a mistress or two, but the testimony of the paintings clearly and unequivocally reveals that he really liked boys. Maybe one of his mistresses posed for his paintings of a clothed Mary Magdalene, but he never painted them with nearly as much gusto as he painted nude Cecco either posing with a love-struck ram in the painting above, or wearing fake wings and sprawling with naked legs akimbo over emblems of worldly power and fame as a laughing Amor.
Caravaggio, Amor Vincit Omnia, c. 1600
And yet, Titian can paint Mary Magdalene wearing only her hair and showing her tits complete with nipples, and everyone takes his sexuality for granted.
Titian, Mary Magdalene, 1533
And Rubens can show boobs busting out all over in his religious work (even Our Lady shows some cleavage here) and no one seems to mind.
Some scholars speculate that an older Cecco may have posed for the figure of Christ in Caravaggio's Supper at Emmaus. The resemblance is striking, round cheeks, auburn hair, pouting mouth; but, if Cecco did pose for this figure, then the painting would have to be dated much later than the 1600-01 date that is the consensus among most scholars. The documentary evidence indicates that this painting was one of Caravaggio's earliest religious paintings, commissioned by Cardinal Scipione Borghese, a patron of Bernini (and would have been a major coup and debut for so young and unknown a painter at the time). Based on that evidence, I think it unlikely that an older Cecco (or a younger Cecco that the very model-dependent Caravaggio somehow aged) was the model for Christ, but it's an interesting thought.