I'd say that first you should work on the fear and skittishness. He needs to build some confidence or catching will be the least of his issues with flyball. Flyball is a very busy, fast, crazy, and loud sport that can completely overwhelm a nervous dog. Are there clicker classes in your area? Clicker training theories are fantastic for building self confidence as they prompt the dog to think for themselves and learn to offer behaviours. They learn that THEY control when the click happens, so it is very empowering for them when they figure it out.
If he is really nervous, I would encourage you to start out with agility before trying flyball. Agility is another great confidence builder and is much less chaotic than flyball, so is a better environment for a nervous dog to get started.
As for catching, start by tossing things that he WANTS to catch ... FOOD! Sit on the floor with a handful of tasty treats. Lightly toss them to him, don't make the tosses very high or very fast. Pretend that you are lobbing a ball to a toddler. If he catches, it is self rewarding. If he misses, quickly grab up the treat before he picks it up off the floor and try again.
After he is consistently catching (or at least trying to catch) food, then switch up to a soft plush toy. They are less "scary" when tossed in the air, and if they hit him it won't startle him as much as a ball would. Again, lightly lob the ball to him, and if he catches it, reach in for a rewarding game of tug or wrestle. If he misses, quickly get the toy back before he can get it and try again. After he is catching a soft toy, then you can try the same game with a ball.