Wow, that sounds like regulation gone wild. I'm all for well-considered coherent policy regimes, but not for conflicting ones with disincentives towards doing the right thing.
Yeah, I understand that point. Governments in general always prefer to see things come in to general revenue. There's a similar fight going on in Toronto about new revenue streams for transportation infrastructure and how to ensure it doesn't get diverted.
The impervious surface fee actually makes a lot of sense, and isn't simply a "rain tax".
Storm-water runoff is a negative externality that right now everyone in a community pays for regardless of their actual runoff. It's a tragedy of the commons - there's no incentive to minimize it. Charging a fee based on the area of impervious surface on a property converts that externality into a direct cost, rewarding those who minimize runoff and charging those who produce the most runoff more. A property owner need only replace impervious surfaces with pervious surfaces and they'll produce less runoff and pay less; everyone wins. It's the same idea as a carbon tax.