Venice is probably the most extreme example, but at least for any other tourism-heavy city I can think of, tourists overall bring far more benefit (economically, even if minor) than problems (annoyance).
Going after cruise ships (as mentioned by Palal above) and tour groups which spend relatively little per person locally are probably the most effective measures. Increasing taxes on hotels and short-term rental apartments is also an option that should be more useful than increasing airport taxes or train fares, as those also affect the people who live there that you are trying to help.
The Swiss have an interesting system for public transportation. You pay full fare by default, but you can buy a 50% discount for a year for $150. Thus, residents most often get this discount while tourists (usually) will pay full fare. Because the Swiss rail system is subsidized for about 50% of their budget by the taxpayer, this also makes it a relatively fair alternative.