I'll go ahead an assume all intransitive する verbs go without を (...right?), but what about the ones that do? Is there a difference in meaning between, for example 料理する and 料理をする? Are there certain transitive する verbs that can't take を for any reason?

I may be wrong, but I understood it as 運転をする being the theoretical textbook correct way of saying it but that in reality, the particle just get dropped most of the time.

I was always under the impression that they are two different things all together.
the +suru part creates a new verb-phrase sort of expression, benkyou suru, unten suru etc

while the + wo part does something else, I don't know I've only really seen /read benkyou suru unten suru everywhere. So I'm just guessing here, +suru feels more phrase like, because you can do wo benkyou suru, or wo untensuru, just like wo <verb>

I think liosama hit the nail on the head. I don't know how your textbook teaches that kind of thing, but here's the most obvious difference:

車を運転する。 -> ok
車を運転をする。 -> wrong. (Actually my IME warned, "「を」の連続" when I typed this example sentence. If you didn't know, ATOK is an awesome IME that is better than MS-IME in every imaginably way. It can analyze your grammar and warns sloppy grammar, informal speech, etc. Ah, but I digress.)

車の運転をする。 -> ok
車の運転する。 -> sounds informal, but acceptable.

Ooh, I get it now! Thanks everyone, this was bugging me for a while.