Probably because checkboxes in real life exist mostly on paper, but when the iPhone came out, the skeumorphic designers wanted to make it look like a sleek device. E.g. the sound recorder app had an image of a big retro-style microphone, and a checkbox would look out of place there.

Probably a button that stays depressed and "lights up" when touched would be more similar to a checkbox. Touch again to uncheck and it will go undepressed.