Well keep in mind that most protein sources, especially that of animal meat, is "acid forming" and needs to be counter-balanced with alkaline forming foods. So obviously someone who doesn't get their fruits and vegitibles but are taking a lot of protein supps are going to have some inherent health issues with it.
It's again another study that's far too vague and near sighted. You need to take a step back and look at a lot of these things and really realize if they're taking everything necessary into account. Especially when the word "average" is thrown into the mix. Obviously none of us are "average" when it comes to eating and working out.