Most of the stores I've worked and shopped in have placed Science Fiction and Fantasy together, usually under the heading "Science Fiction." To the General Public there might not be a difference. Big name authors will usually wind up where they made their "mark". No matter what Stephen King writes it wind up on the horror shelves. If Danielle Steele writes a SF novel is gonna wind up in Romance.
I'm sure there are stores out there who are more stringent and go strictly by content.