When I was in Spain recently it seemed like there was a decent fee for every major tourist attraction (ancient churches etc).  It stung but I was happy to pay as it (presumably) helps the locals.  I wish there was some other way to give more to the locals (would love to tip but also don't want to ruin the tipping culture).

To be fair Kyoto has recovered fiscally since the bankruptcy concerns a few years back. What that really highlighted was that Kyoto is dependent on tourist revenue now.  In spite of, as another poster pointed out, the fact they don't really have the infrastructure to cope with it. And, even if the city is doing OK with tax receipts now, the average resident doesn't see much financial benefit, and certainly not enough to compensate for the disruption people feel to their way of life.