First, there is one major thing you need to understand about how airthrows work: He who jumps first, almost always loses.
Take a guile vs guile match, and say both players are trying to use his backbreaker (which seems to have a better vertical hitbox, while the neutral air throw has a better horizontal hit box).
Basically, whoever jumps first is going to lose in the airthrow war. This is because the character that is the lower of the two, almost always has an advantage in terms of how the hitboxes line up.
But also, you need to know that not all airthrows were created equal. I think the airthow tiers look like this:
Vega, Guile (backbreaker)
Chun, Guile (forward)
Cammy, El Fuerte
And by that I mean who has the superior (i.e. larger and better positioned) hit box.
DO NOT JUMP without a purpose and never jump first against an airthrow character unless you have them at a disadvantage (either by conditioning them, or a safe jump situation).