I'm very familiar with Afghanistan (I spent a few years there as a contractor), and
very familiar with the subcontracting process. The article actually understates the problem.
Virtually 100% of the contracts in Afghanistan which involve transport are contracted to local vendors. Those vendors pay off the Taliban to not attack them; this has been known inside the contracting community ~forever, and publicly since at least 2005. The going rate is about 10-15% of total project expenses; usually it goes from DOD to prime to potentially a sub to a local trucking company to either a relative who is Taliban affiliated, or via a local government/warlord person who is Taliban affiliated.
The risk isn't that random contracts are possibly to Taliban front companies; it is that virtually every trucking and logistics operation (except air) funda the Taliban with a substantial percentage of contract amount.
For the high dollar contracts, or those with substantial on-base performance requirements (e.g. GD/L-3 supplying IT personnel), the prime contract isn't the issue, but the subsidiary support contracts those contractors sign. E.g. when they pay for their living trailers to be brought on base, the trucking company is either closely Taliban affiliated, or pays 10-15% of the trailer contract to Taliban. This means even the big contracts are paying a few percent to the Taliban, indirectly.
The issue is that if the US had zero presence in Afghanistan, none of these contracts would exist. After opium, contracting-related extortion is the major funding source for the Taliban; higher than extortion of the local Afghan economy (other than opium).
If we decriminalized [Afghan] opium, either by buying/destroying or buying/medicalizing (or just decriminalizing narcotics worldwide), and pulled out of Afghanistan, there would be no funding to keep the bad guys going.