Magnets. See the video below.
While the iPad Air (1 and 2) and the new iPad Pro 9.7in are the same size, Apple’s either inverted the polarity of the magnets that grip the Smart Cover to the surface, or simply moved them, so the older covers simply won’t work with the smaller Pro. The cover’s outer flap floats above the surface magically.
This may well go down as one of those inexplicable “Apple things” that leaves people scratching their heads – and a lot of people angry.