Also, we should strip citizenship from anyone who is not a Christian, and punish participation in pagan rituals as severely as murder. This is an ancient idea - Institutes of (Emperor) Justinian in the 6th century are often cited.
What is Justinian's argument? He doesn't actually mention the "commonwealth" at all. He merely appeals to the "law of nature".
In any case, if there is some principle underlying Justinian's edict, what is it? How did he determine that the sea is part of the "commonwealth", but that a mountain or someone's house is not? This is hardly explained in the given quote.
This doesn't really answer your question, but I think it's interesting to note that Institutes of Justinian are doing two things here. First, they are announcing to the Romans that the seas and running waters are part of the commonwealth. Second they are making the seas and running waters part of the commonwealth. They are simultaneously making a declaration and changing the world to fit that declaration.
In short, seas were part of the commonwealth because Justinian said so. An <ahem> appeal to authority. But an appeal that Justinian made, not benjohnson.
He did answer the question: This has a very long historical precedent.
That we continue to accept some historical precedents as good, but have discarded others is not at all odd, and does not invalidate the historical importance placed on access to waterways just because the same people also had lots of ideas we consider idiotic today.
http://en.wikipedia.org/wiki/Corpus_Juris_Civilis
If you want to appeal to authority rather than answer the question, pretty much any Roman emperor makes an odd choice.