Part of making fuel using the Fischer-Tropsch process is actually to turn the coal into CO, which is then used further on in the process. This step is extremely good for removing impurities. All the radioactive stuff is going to be in the ash.

However, using coal means that you are not carbon neutral. It's a lot better to use some process of sequestering CO2 from the atmosphere -- either through plants, or directly. The plant solutions differ from plant oil or ethanol-based fuel production in that the plants are not expected to add any energy to the mix. This makes the process a lot more lenient on what you can stuff in, and makes the drain on agriculture a lot less severe. Also, since the nutrients in the plants are going to be left behind at gasification, they can be reused as fertilizer.