The Case against Cap-and-Trade
This just occurred to me, so maybe I'm missing something but there seems to be another big advantage for taxes: they probably are much more likely to be both tax-burden and progressivity neutral.
Here's why: Both carbon taxes and cap-and-trade would affect consumers by raising energy costs. (Approximately equally, although to the extent that cap-and-trade imposes more administrative costs, you might need to add more to the price of energy to achieve equivalent carbon emissions.) Taxes raise the after-tax prices directly; cap-and-trade raises the price indirectly by forcing producers to purchase credits, which raises the cost of producing, and thus purchasing, energy. Raising energy costs harms the poor most, because they spend more of their budget on energy.
The regressive effects of a carbon tax are obvious because they are direct, so it should be relatively easy to convince Congress to make the tax revenue and progressivity neutral by instituting income tax cuts (and hikes in the earned income tax credit) weighted toward the poor. (And there's a great bargain to be struck here between conservatives and liberals. Liberals can say, "We'll keep it revenue neutral as long as you keep it progressivity neutral.")
But this will be much more difficult to do for cap-and-trade programs. The main reason that Congress might choose such a program over a carbon tax is the fiction that, unlike a tax, it does not impose costs on consumers. This fiction ignores the indirect cost imposed on consumers when the program increases the price of producing energy. Given that animating fiction, it seems like Congress would be less likely to make progressive changes in the tax code to offset the regressive effects of cap-and-trade. (Congress couldn't argue that they were just offsetting the costs of cap-and-trade because their choice of cap-and-trade was based on denying that those costs exist.)