The main concern with nanoparticles is that they are so tiny that they are absorbed into the skin more than we want them (ideally sunscreen should remain on the surface of the skin). Once absorbed they might form unwanted complexes with proteins and they might promote the formation of evil free radicals. But do not panic, these are concerns under investigation. A 2009 review article about the safety of nanoparticles summarizes this, to date, in-vivo and in-vitro studies have not demonstrated percutaneous penetration of nanosized particles in titanium dioxide and zinc oxide sunscreens. The English translation is, so far it looks like sunscreens with nanoparticles do stay on the surface of the skin where they should be.  

The agency makes this exception for several approved color additives. 

Titanium dioxide is used in an enormous range of food products, which can feel jarring when looking at some of its other uses.