These protections are to ensure the FCC / government are always able to decode amateur transmissions. These aren't protections for the operators themselves.
I completely agree with your sentiments though, the amateur bands should not allow proprietary commercialization.
At least with a proprietary codec with that patent restriction anyone can still go out and buy a compatible radio and jump right on. And if the improvement to capabilities is large enough the trade off is worth it. It's not ideal but it's much better than allowing encryption where the transmissions aren't accessible to anyone by design.
Which is not a small mount of money, but isn't that bad given that most amateur radios (excluding the recent Chinese models) retail for ~$500, and commercial radios retail for $1,000+.
That said, I'm pretty sure everyone would prefer to move to Codec2, but the lack of hardware offerings is a problem. I'm looking forward to the day the first real SDR handheld transceiver comes out so this can be implemented by the open source radio community. It's clear that none of the radio manufacturers are interested in interoperability, much less adopting community standards.
Except that proprietary voice codices are allowed :(