Because wind only blows sometimes, and the sun only shines sometimes, any solar or wind installation requires backup generation, usually natural gas or coal. While natural gas produces less carbon emissions than coal, it is not purely "clean." Natural gas produces about half the carbon emissions of coal. You can also check out the additional economic costs of wind due to backup power outlined here.
And, when these fossil fuel backup generators cycle on and off-- as needed in a backup capacity for an intermittant renewable-- both natural gas and coal are necessarily less efficient and produce even more carbon than usual. In fact, studies performed by Argonne National Lab (which Obama just visited last week to talk energy) showed that wind did not meet carbon emissions guidelines because of the inefficient way it forced backup sources to work.
Solar or wind installations = fossil fuel installations.
Fossil fuel backup = carbon emissions.
Since wind and solar (and any intermittent renewable) necessarily require backup, the carbon tax on that backup means a detriment to wind. From the Chicago Policy Review only a few months ago:
In a new working paper from INSEAD, “Strategic Investment in Renewable Energy Sources,” researchers Sam Aflaki and Serguei Netessine were surprised to find that taxing carbon emissions from fossil fuel-based electricity generation did not necessarily improve the long-term competitiveness of wind power investments. The researchers found that intermittency issues related to wind-generated power are... too common to allow wind generation to price independently of the fossil fuel market.Batteries unfortunately can only provide backup for wind or solar for about an hour at a time, even at costs of millions of dollars (see Duke energy's $44 million wind batteries)... and batteries have their own environmental impact.
It is a good thing that we have a cheap supply of domestic natural gas, which does burn cleaner than coal. However, the only way to produce significant amounts of reliable carbon-free energy that is technology-ready now is through nuclear energy.