Hugpug is right, you can only activate an AP voucher at Guest Relations or at a ticket window at one of the four theme parks, or at Guest Relations at Downtown Disney.
The airport Disney stores can NOT activate a voucher; they only sell new, fully-activated APs.
Hugpug is also right that some CMs at check-in give you a hard time about the AP rates if you have not yet activated your voucher. However, if this happens, politely but firmly insist on seeing a supervisor, and explain in no uncertain terms that
A) an AP voucher is absolutely, completely, and in all other ways, NON-REFUNDABLE, so having one prooves beyond a shadow of a doubt that you have already paid for your AP but simply have not yet activated it. Don't take no for an answer; an AP voucher is rock-solid, undeniable proof that you have already forked over a lot of money to WDW for your AP, and since it's impossible to return the voucher under any circumstances, you cannot possibly be pulling a fast one to get the cheaper rate then return it, so the resorts darn well better honor the AP rate that you booked.
B) You've been travelling for about 6 days without sleep, are totally exhausted and in need of a rest, a meal, and a shower (not nessicarily in that order), and you are simply too tied to go all the way to one of the activation points before check-in.
Don't worry about this too much, however. CMs who don't want to honor your AP rate are few and far between; in fact, I have not heard of this situation coming up for quite a while (over a year). Even when it did happen, the supervisors always gave in when the AP holder pressed the matter and explained (calmly, without any yelling or threats) what the true situation is with a voucher.
