Rather than providing a subsidy as an incentive, I am more in favour of having a price on pollution. In a perfect market, all externalities of an economic activity should have been accounted for. Therefore the most viable and rational option will surface. Ideally, markets should function in that manner. If Governments spend their effort to put a price on carbon, that will help the industry to switch out of their current free riding on other people's woes and provide the right incentive for clean coal and other alternative sources energies to be economically viable.
The good thing about putting a price on carbon is that it can be self regulating. If clean coal is not as clean as claim and not as efficient as thought, market forces ought to be able to push that technology out of the market and replace that with the next best alternative. The pitfall of subsidy is that market incentive will get distorted and resources will be required to regulate and monitor the use of the subsidy.
It also mean that base on current level of understanding we have picked our winner. More often than not, once the winner is picked, it is difficult to argue against it and difficult to adopt a competing alternative, especially when significant public money is involved.