It was a trademark application, not a patent application; Harley-Davidson claimed that the sound made by their engines was distinctive enough to act as a "source identifier" to consumers.

A bunch of other manufacturers filed oppositions to the filing, basically pointing out "Hey, we also make large-displacement, common-crankpin 45-degree engines and guess what - they sound just like yours."

H-D gave up after 6 years and some litigation, but they probably wouldn't have been successful anyway - you can't trademark *functional* aspects of a design, and the "Harley" sound just comes from the mechanical characteristics of the engine.