I also don't believe it has anything to do with the cable. The same cable that works to charge the controller from the console won't work with a standard charger or port on a laptop. Those same chargers and laptop ports work to charge anything else. I also don't think I've ever encountered a data only USB cable. I've definitely had some that provide power, but don't work for data. I can even imagine intentionally producing a cable like that to be used exclusively for charging. However I can't imagine many cases where I'd be able to use a cable that only provides data lines.
You're suggesting that a PS3 controller can only be charged using a port that the Playstation 3 never had.
However plugging a USB 2 cable into a USB 3 port will certainly work because the latter is backward compatible. Hence if the PS3 controller were able to charge off something other than a Playstation 3 it would be able to do so off the newer port as well, using a USB 2 cable.