I haven't looked into Protong in depth, but at a first glance, it looks it takes some lightly motivated ideas as substrate and builds pseudoscientific nonsense on top of them.

The idea that all human language stems from a common source is not an uncommon hypothesis. This hypothetical language is sometimes called proto-human or proto-world, and there have been some attempts at reconstructing it, but it's also not a slam-dunk in terms of evidence: other linguists believe in linguistic polygenesis, which is the idea that there were multiple independently-evolved ancestor languages, and both positions have some evidence for them. Still, there are linguists who believe in it and are working towards understanding what it might have looked like.

Any specific reconstruction of proto-human, though, is difficult, and would need to be subjected to a pretty rigorous set of criteria. There have been attempts along these lines, sometimes using statistical methods, sometimes using comparative reconstruction (which is the linguistic technique of extrapolating a common ancestor between multiple related languages), but languages change a lot—especially if they don't have a written language, which was the norm for most world languages until recently—so merely extrapolating a few hundred years back can be difficult and involve a lot of guesswork and masses of evidence. Going tens of thousands of years back is truly grasping at straws, and as such any proposal along these lines is going to have to be as bulletproof as possible. (Indeed, a large number of linguists believe that enough information has been lost since a proto-human language might have existed, that such a reconstruction is in fact impossible!)

Protong specifically looks like it involves a lot of playing with semantics in a way that doesn't match what we know about how languages evolve. There's a lot of, "Well, this language has a word that sounds like this and means 'murderer', and that language has a word that sounds like this and means 'run', and you run from bad things and also murderers are bad, so that's a proto-word that means 'bad'." That's not how language evolution works, and if you accept those kinds of arguments, you could make just as convincing a case that any language has any relationship you want to any other language! The classic example of this is from the Dutch physician Johannes Goropius Becanus, who believed that the original primordial language as spoken in the Garden of Eden was his native dialect of Antwerpian Dutch: for example, he suggested that the name Adam came from the Dutch Hath-Dam, or "dam-against-hate". If you can use your argument to "prove" that Biblical Hebrew was descended from Dutch, then you're not using a robust argument.

And to address the original question: if we have such difficulty reconstructing a proto-language now, with our wealth of collected and available knowledge, it would have been an impossibly difficult task in a Europe that had not yet deciphered Egyptian or had extensive contact with the New World. Consequently: even if the monogenetic hypothesis of language is true, and even if proto-human is a reconstructible language (whether it resembles Protong or not), it would be vanishingly unlikely that a person or group of people had managed to reconstruct it with enough accuracy that they could write an entire manuscript in an invented writing system that happened to mirror it. Given all this, I'm absolutely confident in saying that the Voynich manuscript is not in Protong or anything like it.