That depends. Under 10% will end up as private practice doctors. A good 40% or so according to some stats I've seen will end up in clinical academic departments. At this point it's questionable exactly how much of their job is clinical, research, administration, and/or teaching.
The pay for private practice docs will be the same as that for MD. The pay for academic physicians will be maybe 1/2 to 1/3 that, depending on specialty. The pay for basic science research will likely be even lower until you get established. Pharm company MD/PhDs will probably make as much as private practice docs, but again it depends on the situation.
The moral of this story is, on average MD/PhDs (80%+ in academic medicine/research) are going to make a good deal less than MDs. You have the potential to make the same amount, but then you've spent more time in training to make the same amount of money and private practice is not what the MD/PhD is meant for. A small percentage will go into the industry doing trials or trying to design new implements or drugs and will get paid relatively well for a MD/PhD, again depending on too many factors. Nevertheless, I'm not going to argue industry vs. academia, but it's not a large percentage of MD/PhD who do the industry path.
