Institute director, Peter Martin, stresses that his research group wants to maintain "arms length" from the coffee industry for ethical reasons. "We are setting up a foundation to oversee the funds which will be administered by independent scientific directors to ensure that there isn't even an appearance of conflict of interest," he insists.
In addition, the original article described a wide variety of studies done by many different institutions. I suppose it's possible that they're all just "studies" conducted by people in the pay of the nefarious coffee lobby, but we probably shouldn't start resorting to conspiracy theories without a little evidence.