I may be on the odd side of this debate, since I think fossil fuels are useful due to their insane energy density and easy transportability, which is why we have used them for so long. I also acknowledge the fact we need an alternative since our fossil fuel supplies are limited. I do think such an alternative will come about without the government needing to shoehorn money into research. Currently solar cells are too expensive to be of much use. If someone makes a cheaper, more efficient solar cell, just think how many people will want to buy them. I know I will due to the fact they will be able to provide cheap, clean electricity. Who wouldn't mind a car that doesn't need to be constantly refueled/recharged? A pure electric solar/plug-in hybrid would be a great method of efficient energy, especially if more fission power is utilized for electricity. I don't see wind farms being of much use. They require lots of wind and lots of space. They are far more limited in their application than solar cells, which can be placed anywhere that receives sunlight. Tidal generators on the other hand are much more viable due to the fact the Earth is 70% water, and tides have more energy in them than winds.
To be honest, if someone develops working fusion, I can see research into synthetic fossil fuels being undertaken as they are more energy-dense than batteries and with proper treatment of exhaust gases, can output very little pollution.
I think there is very little need for government funding of alternative energy supplies, as there is too much benefit for the private sector to not develop them. There are private energy businesses besides Big Oil after all. And anything government-related can quickly become politicized and full of corruption and waste. In the private sector, there is less waste as every dollar that is wasted is a dollar that won't be profit.