+John Voelcker at +Green Car Reports wrote a good piece that refutes much of the concern about these batteries from the perspective electric vehicles. In short not all lithium ion batteries are created equal. There are different chemistries available with unique characteristics. The cobalt-oxide cells used in the 787 have the highest power density, but they are less stable and more prone to thermal runaway and fires. 

John points out that most plug-in vehicles do not use cobalt-oxide cells. For example, the +Chevrolet Volt and +Ford Motor Company Focus Electric batteries are filled with manganese spinel cells while some other vehicles use iron phosphate chemistry all to ensure safety.

There is however, one very important exception. +Tesla Motors has opted to use cobalt oxide cells in its batteries for both the original Roadster and the new Model S. +Mitsubishi Motors North America iMiEV has a battery produced by 787 supplier GS Yuasa although I'm not sure what kind of chemistry it uses. +Honda also has a joint venture with GS Yuasa to produce batteries for its plug-in and hybrid vehicles, but again I'm not sure of the chemistry.