No, autographs at the pro shop or other seahawks sponsored events don't charge that I know of. usually those are just at card shops/personal appearances.
Most of the time that money goes to the store. It's also a deterrent from the line being full of merchants just looking to get stuff to ebay. If you have to pay for it you must really want it for yourself and aren't going to turn around and re-sell it, so i don't usually mind if you do need to pay for it. percy harvin just had a signing in mill creek and it was a pay one, I don't really think he needs the money so I'm assuming he wasn't pocketing all of it. I wouldn't be surprised if under the CBA or other NFL rules they required the store to reimburse him for his time/travel etc. since it wasn't hawks/league affiliated but I doubt he thought he would just scoop up an insignificant wad of cash out of greed.