The tech behind these toys involves conductive plastic that interacts with the iPad's touchscreen similar to finger touch. The figurines and other Apptivity objects won't scratch the display, but if you're still worried they'll work even if there's a screen protector on.
There are dozens of accessory and case makers in the world attempting to solve the problem of protecting your precious iPad or Android tablet from the pitfalls of modern life.
Some solve this by wrapping it in armor or gel or just mounting it to a stable surface, never to move.
Some solve this by wrapping the tablet in balls.