It's the author conflating "Linux" and "open source". In their statement, Proton states "Linux community" snd the author promptly writes "open source community". Knowing the difference between the two seems like a requirement to write for a tech publication, but maybe that's just my crazy opinion.

The venn diagram doesn't need to be perfectly overlapping circles. When open source is not a viable option or you need something beyond the scope of what open source offers, the next best thing is to use a product from a reputable company that has been properly audited and has not completely enshittified.

Now, whether Proton is truly that company is up for debate. The CEO has made some pretty troubling comments, but the products themselves have not devolved all that much. You can probably find better than Proton, but you can absolutely find a hell of a lot worse.

What is a proprietary protocol? Is that like mpeg where everyone knows how to implement it but you have to pay them to use it?

I think the protocol was developed in-house and only the code is open source? I think the protocol itself is not public to make it harder to spot, since its whole purpose is to dodge deep packet inspection