It's not so much that fossil fuels are preferred, it's more along the lines of fossil fuels are needed. I dare to say that over 90% of all the combustion engines in the world right now where designed with the mindset of using fossil fuels as their choice of fuel.

Let's assume that you have a diesel engine car, and you decide to use another type of fuel, let's say biodiesel, you'd have to change one or two things in your car before it would work without causing any problems(e.g your fuel pump and fuel filter) and you wouldn't even be able to use pure 100% biodiesel.

Don't forget the fact that fossil fuels are actually cheaper than alternative sources of fuel. Biodiesel for instance is more than 1$/litre as opposed to diesel which is roughly half of that in Nigeria.

Using fossil fuels are cheaper and at the same time require no augmentation of your combustion engine. At this point in time they are preferred, but maybe in the near future, as global warming laws become more stringent all around the world, we just might see a change.