One of the major reasons for 100-400 is for the flexibility and length. IQ wise, it definitely doesn't beat a 500 prime, but it gives you the option to zoom in and out, which can be important when you want to frame formation shots. Of course, that depends on how close you are to the planes. Also, I find hand holding the zoom for 4 hours is tiring enough (you really do need to hand hold if you want all the angles), much less a 500mm. I was in the crowd for Fleet Week, so even with a 100-400, I had to be very careful not to whack anyone in the head with my lens when I try to track the planes. A kind old man had to duck twice because I got a bit caught up chasing the jets... so again, a 500mm in that situation would just make it all the harder.
Great shots are like great parking spaces... if you're not quick, it's gone!