There are a lot of speculations over why the Air France flight crashed in 447 in the waters of the Atlantic Ocean. Here is a detailed meteorological analysis which concludes:
Overall what we know for sure is weather was a factor and the flight definitely crossed through a thunderstorm complex. There is a definite correlation of weather with the crash. However the analysis indicates that the weather is not anything particularly exceptional in terms of instability or storm structure. It's my opinion that tropical storm complexes identical to this one have probably been crossed hundreds of times over the years by other flights without serious incident.
Still, in the main MCS alone, the A330 would have been flying through significant turbulence and thunderstorm activity for about 75 miles (125 km), lasting about 12 minutes of flight time. Of course anything so far is speculation until more evidence comes in, and for all we know the cause of the downing could have been anything from turbulence to coincidental problems like a cargo fire.