Exactly. I was going to post essentially what you did.
An article linked from the POGO site quoted a trade rep: "The fact is that POGO's report draws false conclusions by comparing fully burdened contractor rates — which include all costs charged to the government, such as salaries, benefits, overhead, supplies, equipment, materials, rent and more — to an estimate of just salaries and benefits paid to a similar government workforce,"
I am a federal contractor and I guarantee no one billing the government on our contract makes the kind of money alleged by POGO. We work in our own facility, we buy our own equipment, provide our own IT support, plus the overhead people (HR, senior management, for example) are paid from what the company bills for my time.
As you stated, a fair comparison would be to factor in what the government pays for its facilities, equipment, executives, employee welfare, insurance. Also, it's impossible to get rid of a government employee. If we don't perform, though, they can terminate the contract.