I do not believe that the observation deck at the Wilderness Lodge is open to the general public. From what I've heard it is only used for the Family of the Day program.
The last time that we went to Disney was 2 years ago. We stayed at the WL and got to be the Flag Family. You get to the top by elevator as far as you can go and then along a walkway at the top of the lodge ceiling. I really don't like heights and it was a little nerve racking. The view was worth the whole thing. It was beautiful you could see forever. It was on the last day of our stay and it is probably one of our best memories.
We did the flag raising thing seveal years ago ... found out about it byaccident at the front desk and got lucky. I also believe this is the only way up top ... not set up for crowds.
I saw something like a secrets of the Lodge tour at the front desk, thought maybe they'd take you to the roof on that. Sounds like only the family of the day gets to do it, I'm jealous.