Prospero (and Miranda) is as kind as possible to Caliban, but there are limits. And even after the attempted rape, they’re still kind to him. Consider: If you were on a deserted island with nobody but you, your daughter, and a single native, and the native tried to rape your daughter, be honest here: Would that native have lived to see another sunrise?
One symmetry I’ve always liked about The Tempest: Of Prospero’s two main servants, one is corporeal and one is a spirit; one is natural and one is supernatural. But the natural one is the spirit, and the supernatural one is the corporeal one. There’s nothing at all unnatural about Ariel-- He’s the storm and the lightning and the gentle breeze. Caliban, though, is a demi-devil bastard.
You can also look at the differences between Sycorax’s and Prospero’s ways of dealing with the world. Sycorax is genuine slave-driver: When Ariel can’t or won’t do her will, her response is to imprison him in an oak. Prospero, though, started by freeing him from the oak, and winning his respect and (insofar as such is possible) love.
The most interesting strings are the ones he doesn’t pull using magic. He probably could have cast a spell to make Miranda and Ferdinand fall in love (that wouldn’t be so different from Oberon’s love potion in Midsummer), but he doesn’t, instead manipulating them through purely mundane means.