Even if you include that crash in the numbers, the safety numbers are still incredible. Something like 10 passenger-light-days per fatality. Quite lumpy though, with the median deaths per year being 0, and the average number of deaths being 5-10.
Good news is that air travel is getting radically safer. If you do the "flight passenger light year" math for 1980-2000, you only make it a few light-hours per fatality, and for the 20 years prior to that, it was about 50 light minutes per fatality. Still safer than cars, on average (although some cars are much safer than others, and a lot of your risk depends on driving habits).