It is technology driven. It could be characterized as a mechanized vs. non-mechanized conflict. PWCs are so incredibly noisy, fast and intrusive compared to some boats that boats could be almost considered non-mechanized in comparison. Most PWC users do not have boats. Most boaters do not have PWCs.
Some boating articles indicate a large percentage of PWCs are owned by boaters.
If boaters own them, it is hard to imagine they are the ones complaining. Much of the conflict occurs between city dwellers. Rural recreationists tend to have higher tolerance for alternative behaviors. Many people now on the water from both groups are from cities. Boaters tend to be older.