The people at Rate it all seem a little geographically challenged. Their top-rated San Francisco attraction is … the Monterey Aquarium (although on the basis of only 4 ratings).
The other leaders, in order:
Golden Gate Bridge (118 ratings)
Golden Gate Park
The only other museums to make the list are the Maritime National Historical Park and the Cable Car Museum. No deYoung, no Legion, no Asian, no Cartoon Art Museum, no Museum of the African Diaspora, no Contemporary Jewish Museum, no Oakland Museum, no Cantor Center, no Zeum, no Historical Society, etc. The Steinhart Aquarium did get two ratings.
If you are planning to be a tourist, other tourists might not necessarily be the best people to ask for suggestions about what to see.