The recent decision didn’t so much “strike down” the protections, but rather ruled that the relevant law does not apply to the wetlands the EPA used to apply it to. There was previous ruling, which according to SCOTUS, was erroneous, and so it reversed it.
This is perfectly reasonable if you look at the original law and intent behind it, and the wetlands the federal agency no longer can claim control over. The original law was passed to protect the “navigable waters of the United States”. The agency claimed that wetlands around random creek flowing into a lake are covered, because there is a “significant nexus” between it and some navigable waters, somewhere. If you disagreed, tough luck, your best option was to appeal to the same agency, making it both judge and prosecutor in the same case, and in any case is not a practical option for a random person without deep pockets, who just want to build a house on a lake.
The ruling said that when the law says it applies to navigable waters of United States, you can apply it only to waters or wetlands that actually are navigable for purposes of interstate commerce, or are so connected to these waters to be practically indistinguishable. This is perfectly reasonable: if given wetlands are not connected to interstate navigable waters, why should they be under federal jurisdiction in the first place, especially given the plain language of the relevant law? If the state wants to protect its own waters and wetlands, it’s certainly free to do so.
Now, I believe that federal government could actually argue that the random wetlands actually can be under its jurisdiction, if they affect the water in other states, eg. through ground water flows etc. However, they will need to pass a new law to assert that, instead of leaning on old law that clearly did not mean to cover this.