"Who are you looking for?"
I think it might be related to context! You see someone crawling around you might as well ask What are you looking for? As it's an obvious continuous action you are probably going to use 在 in this situation!
On the other hand, a secretary might use "你找谁" when you come in, without 在, because it seems to be a point action: you come in and ask, period!
I might be wrong but that's my reasoning for now!
Maybe a more direct translation could be "Who do you look for?" But that doesn't sound natural for me!
Of course preposition means 'to place before', and in Latin they truly must be before. However in Germanic languages prepositions can very naturally come at the end of a sentence and the 'rule' that they can't was a ridiculous attempt to impose Latin grammar onto a Germanic language (as with 'split infinitives', etc). 'Whom are you looking for' is a perfectly natural English sentence, and in fact what I would say.