And herein lies the rub of USB-C: It isn't a universal logical interface, it is a multi-use physical connector. By overloading the port's logical functions you introduce incompatible physical configurations.
There have always been charge-only USB cables, they're just not all that common (I believe many mice come with those for charging, but I don't know where else you'd get one). I agree that it is a problem for Apple to be shipping a charge-only USB-C cable, both because this significantly increases the number of charge-only cables in the wild, and because this is probably the first USB-C cable that their customers will have and it's confusing if it doesn't actually act as a generic USB-C cable.
Charge-only Mini USB connectors are a different question. They're possible to build, but non-compliant. Charge-only USB C cables are part of the standard. The difference is that you can only blame cable confusion problems on the standard in the latter case.