Litium ion-batteries are great, and safe for automotive use. Draw-backs are that they are still relatively expensive, sensitive for being discharged completely, sensitive for overcharge, and require some kind of battery management system, monitoring and controlling each cell. Most are also limited in charge/discharge rate, which I think is the second reason hybrids still use NiMH-batteries (cost is main reason probably). It's tough for a 1 kWh battery to handle charge/discharge power of 15 kW, during many years of use.

If litiums weren't safe I wouldn't trust millions of people carrying them around in their cell phones, cameras and laptops.

Rumours has it that Toyota plan to use litium-ions in their next generation Prius. Let's hope it happens soon, it would be a real break-through for the technology.