The tone is one of instruction and caution, like a fairy tale. In fact, if you look at the title, you will see that its complete title is "A Very Old Man with Enormous Wings: A Tale for Children." Upon first reading, you may think this is the *last* thing you'd want to read to your child! But think of the stories of the Brothers' Grimm. Those tales also were gruesome but contained some moral lesson, created not only to excite but to instruct.
The villain and the antagonist can be considered in two ways. First, Pelayo and Elisenda treat the angel miserably. They do not appreciate in the least this miraculous being. They cage him like a farm animal and exploit him for money. The people of the town are no better. They eagerly come to view the angel and pay for a glimpse at the poor creature. Even the priest, Father Gonzaga, is more interested in seeing if the angel meets his prescribed tests, such as speaking Latin, instead of appreciating the miracle.
There is no human protagonist in this story. The angel himself may be considered so, as he does nothing wrong and finally escapes his mistreatment.