I've heard that its because your heart skips a beat when you sneeze, so people in the old days used to say God bless you because it was as though they'd died for a second. Its a bit exaggerated for death, but I believe that's the reason behind it. Farting however, is just a natural byproduct of digestion, so there's no need to be blessed for simply doing that.
When you sneezed in the olden days it was believed you could loose your soul by sneezing so if you were blessed "god bless you"straight after sneezing it saved your soul. But when you phart who is going to bless you for dropping your guts in public.