I am not aware of any patristic commentary on the proto of james. perhaps some exist which gives reasons for it's exclusion. I tend to doubt whether there is, but i suppose it's entirely possible. the book does have some historical value, but we must assume that it was not actually written by the person known as James brother of Jesus as is claimed, and this fact alone would most likely be sufficient for disqualifying it for entrance into the canon.
I don't see the question of its human author as particularly relevant. For example, consider the question of who wrote some of the letters traditionally attributed to St. Paul. Now, I myself believe that St. Paul wrote all of them (excluding Hebrews, which I choose to believe, admittedly without any good reason, was written by St. Barnabas). But if it turns out that some of the pastoral epistles were written late in the 1st century by some disciple of St. Paul's then I don't see that as having any bearing whatsoever on the question of their inspiration. We know they're inspired, because the Church has canonized them. The flip side of that is that we know the Protoevangelium is not inspired, because the Church didn't canonize it. And even if the book really was written by James, that doesn't mean it was inspired. Not in the least.
For comparison, consider that we know there's at least a third letter of Paul's to the Corinthians which is not in the canon. If that third letter had been inspired, it wouldn't have been los--it would have been canonized. So even though it's a letter of Paul's it's not inspired. Similarly, there could be a book of James's that was not inspired.