Even though I'm disturbed and freaked out by the kissy smiley..
The only time I dock them is when they've gotten so beaten up that they're mostly ineffective (like if you only have 1-2 fighters left out of a squad). Docking them keeps them safe while they rebuild, because otherwise you'd just keep losing the one measly fighter over and over while fighting and the squad won't replenish until the battle is done.
This is only really useful early on when you don't have 50+ squads zipping about, though. Then you just tend to not care about single squads much.
Conceivably, there are some capital ship abilities that make life rather hellish for strike craft but the AI doesn't really use them much (and I don't play MP) so even though docking would spare the craft until those capitals are done, I never had to do it.