I disagree that "... you didn't ask" means someone has already asked the question. If that were the case, it would be "I rather you hadn't asked that" -- actually, we would usually say, "I wish you hadn't asked that'
I don't think there's a big difference between the two. I think it might be regional or geographical -- for example, one might be preferred by British English speakers.
"would rather" is usually followed by past tense when you add another person (I'd rather you... I'd rather she....)
I'd rather you didn't do that
this is from the BBC Learning English site: .....
http://www.bbc.co.uk/worldservice/learningenglish/grammar/learnit/learnitv107.shtml...
Would rather (but not would prefer to) is also followed by a past tense when we want to involve other people in the action, even though it has a present or future meaning. Study the following:
Shall we go out for dinner tonight? ~ No, I'd rather we ate at home, if you don't mind.
Shall I write to Harry and tell him that we've sold the car? ~ I'd rather you didn't.
My mother would rather we caught the bus, rather than walk home after the party.
---------
I just want to add that if someone asks something that you don't want to answer, just say "I'd rather not answer that' or "I'd rather not respond to that."
(of course, you can always say, "That's an inappropriate question." :-)