Yes, I always tell visitors to be prepared for a letdown when their train pulls into Kyoto Station. No samurai, no geisha, not even a rickshaw!
The delights of Kyoto are found in a few well-preserved neighborhoods, the historic and religious sites, and in serendipitous discoveries on obscure side streets. I advise visitors to get Diane Durston's Kyoto: Seven Paths to the Heart of the City, which lays out walking tours of the most interesting areas.