These questions have come from a number of places around the net.  Some are from our community and others come from different discussion boards & forums. 

1) City walls in C & K: It states you get 2 extra card limit for each city wall and "City walls protect your cities from the robber." What does protected mean in that context?

"Each city wall that you control increases the maximum number of cards you may keep in your hand if a "7 is rolled on the production dice. Each wall adds 2 cards to this limit."

2) You have the Aqueduct and there's a robber on your wheat production with a 6 on it. If a 6 is rolled, do you still use the Aqueduct powers?

You use the Aqueduct powers when anything but a 7 is rolled. In this case, assuming you have no other production on a 6 either, yes, the aqueduct allows you to take a resource of your choice.

3) Commercial harbor progress card: If you offer a resource card and the target opposing player doesn't have a commodity card, is the transaction null and void or are you screwed and lose that resource to the target player?

"If you offer a trade to a player who has no commodity cards, then the trade is void -- you do not have to give that player the resource card."

4) Merchant fleet progress card: So is the 2:1 like the generic ? port or do you declared a resource or commodity and only trade that for 2:1?

"... and with as many different resources and commodities as you choose."