Susanbrindle's basically got it. In relative terms, attack craft are a cheap way of doing serious damage to enemy ships and bypass their shields. Fighters are defensive tools. And since not many people use them, not many ships are outfitted with extensive point-defence arrays (and canny tricks like sending fighters in with bomber/assault boat waves mean you can swamp the turrets of most ships anyway).
If your ship has the capacity, a really good trick is timing your attack wing's bombing run to coincide with an incoming torpedo salvo, as turrets have to choose whether to aim for the fighters and bombers this turn, or the torpedoes. They can't go after both…
Also remember, you've got the capacity to house 3 squadrons for every point of launch capacity the bays give you. You can only launch a number of squadrons up to and equal to that point capacity, but in theory you can do that for three turns without needing to recover craft.
In practice, you've got to balance squadrons of fighters, squadrons of bombers/torpedo bombers, squadrons of assault boats, support squadrons (SAR birds, cargo shuttles, VIP transports) and Aeronautica (anything designed primarily for atmospheric work, usually with rocket boosters for orbital launch and recovery).
That balance is a matter of personal preference (I always reserve 1 squadron slot for support craft, and if there's more than 2 Launch Capacity, I make sure another squadron slot is reserved for Aeronautica. Then roughly half the remaining squadrons are fighters, with the balance of bombers to assault boats determined by how many troops the ship carries).