Composites such as Glass or Carbon Fiber are difficult and expensive to repair and not a lot of people have experience. They also don't absorb energy like metals making crash safety an issue. A major benefit of carbon fiber in aerostructures is fatigue and corrosion. Composites don't fatigue like aluminum and this means the differential cabin pressure can be much higher vs. aluminum making a much more comfortable environment especially on long haul flights. The humidity can be much higher as well. If anyone has flown a 787 long distance they know what I am talking about.
As sld mentioned, mating aluminum and carbon fiber needs careful design attention. Often titanium is used instead of aluminum to mitigate galvanic issues but this is an expensive and usually heavier option.
I suspect composite usage in ground vehicles will continue to increase especially as new manufacturing processes are developed and refined. Additive manufacturing is changing things as we speak.
You bring up a good point on the composites not absorbing energy like metal. I wonder if that is one of the reasons (other than weight savings) that Ford went aluminum.