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.
Last year Identity Games launched the GameChanger, a clever blend of traditional board games and the iPad. This year the company is expanding on the idea — or, I should say, shrinking it. At Toy Fair they showed me an early version of the GameChanger XS for the iPhone and iPod touch.