This was a report by a consumer watchdog organization. The industry asked for and got an independent review by NSF/ANSI, which basically a third party non governmental testing group. It passed their testings. The consumer group also reported that there were varying levels in samples, and not all samples produced the same results.
That being said, I would classify the protein drinks kind of like the Hitchhikers entry for Earth - "Mostly Harmless". If you need a quick drink or are behind on protein intake for a day, then I have no problem drinking any protein drinks. If you find yourself needing it long term, then I would assess your diet plan to see why you are always coming up short on protein needs.
There are also some concerns about the presence of aspartame, which breaks down in the body to formaldehyde and...formic acid? These have been known to cause migraines and other health complications. Also, heavy metals don't flush from the body easily, so if you continually have high intake, you could potentially see some complications.
My best advice when you see something like this is to garner as much information from reputable sources, and consider the original source. The consumer watchdog group's prime reason for existence is to sell the results of their surveys. Their article even states that not all samples produced this, but it's a one liner tucked away from the blaring graph of the ones that DID have detectable levels.