ORIGINAL: SeaQueen
I don't think it's that bad.
I've heard Command sometimes referred to as "death by options," which is unflattering, but not necessarily untrue. In the beginning you probably won't use most of them, though. Instead you'll start off relying on defaults. Eventually you'll start monkeying with things like, "I don't want my fighters to mess with helicopters, I want them to focus on bombers and 5th gen aircraft." All the options allow you to really sculpt the AI's behavior and intelligently manage increasingly large scenarios.
I think the best way to learn it is to work through the tutorials, but then focus on the things that are really interesting to you and make your own small scenarios, then branch out from there.
IMHO, the options are part of the Mastering the Game part of Command. You can start out with the defaults but as you become more sophisticated and look under the hood at what's available to you it becomes apparent that a very high-fidelity experience is there for when you want it or are ready for it.
