The logic behind the fees is essentially the same as a Pigovian Tax:
http://en.wikipedia.org/wiki/Pigovian_tax
It may not be "fair" but it results in widespread modification of behavior in a socially beneficial way.
Taxes on carbon fuels are not fair -- lots of firms built up huge infrastructure on narrow profit margins before such taxes were imposed -- but if you advocate a different policy what would it be? Every policy entails some "transfer" from one group to another. At least with a tax the incentive is clear and obvious moving forward, and precisely targets the specific negative externality it's intended to address.
