There was a good thread on this two years ago, pointing out several things Atwill missed. To quote the answer I gave there:

I read through a lot of this, and now I want my time back. This is an advertisement written for the popular press, so it can't really be analyzed like a scholarly work. However, it poses questions that have already been answered for millenia and neglects well-known contradictory facts. Here're a few of his points with rebuttals.

Who wrote the Gospels? Why are they written in Greek?

This's been well-known and acknowledged ever since the early Church. The Gospels were written decades after Jesus' death, not to proclaim Jesus as Messiah to Jews, but after Christianity had already spread to large numbers of Gentiles. So, they were written in the common language of the Eastern half of the empire - Greek.

In order to pacify the Jewish rebellion, they [the Flavians] captured and burned all the Jews’ scriptures.

Wrong. According to the Talmud, the Romans even allowed the Sanhedrin to continue meeting at Jamnia. Whether or not that's the case, rabbis continued preaching without disturbances at least until the Bar Kokhba rebellion sixty-five years later.

It is around this time that a new literature emerged with the story of a very different Jewish Messiah

When the Gospels were written is a disputed subject, but what isn't disputed is that Christianity arose well before the Jewish Revolt. For example, the historian Tacitus records Nero blaming the Great Fire of Rome on Christians, commenting:

Christus, from whom the name had its origin, suffered the extreme penalty during the reign of Tiberius at the hands of one of our procurators, Pontius Pilatus, and a most mischievous superstition, thus checked for the moment, again broke out not only in Judæa, the first source of the evil, but even in Rome, where all things hideous and shameful from every part of the world find their centre and become popular.

Similarly, the historian Suetonius says that the emperor Claudius expelled the Jews from Rome due to their infighting about "Chrestus."

So, in short:

• Well before the Jewish Revolt, Christianity not only existed but had spread to Rome.

• The Romans did not try to rewrite the Jewish religion after suppressing the revolt.

• The Gospels were written in Greek for well-acknowledged reasons; we need not search for conspiracy theories.

"Is this the beginning of the end of Christianity? "Probably not," grants Atwill, "but what my work has done is give permission to many of those ready to leave the religion to make a clean break. We've got the evidence now to show exactly where the story of Jesus came from. Although Christianity can be a comfort to some, it can also be very damaging and repressive, an insidious form of mind control that has led to blind acceptance of serfdom, poverty, and war throughout history. To this day, especially in the United States, it is used to create support for war in the Middle East."

Guy seems to be a conspiracy-theory hack with a clear political motive. The article calls him a "biblical scholar" but researching him a bit shows that he's not really a professional at all.

I also have additional questions about this. If Christianity were a product of the Roman State, why were early Christians persecuted by the Roman state? This seems counterproductive.

Atwill also says this:

"When the Romans had exhausted conventional means of quashing rebellion, they switched to psychological warfare. They surmised that the way to stop the spread of zealous Jewish missionary activity was to create a competing belief system."

Have we known the Romans to engaged is such sophisticated psychological warfare elsewhere? If this were a tactic of the Romans, surely it would have been used in other places around this time.

This part of the article is really concerning to me:

How could this go unnoticed in the most scrutinised books of all time? "Many of the parallels are conceptual or poetic, so they aren't all immediately obvious. After all, the authors did not want the average believer to see what they were doing, but they did want the alert reader to see it. An educated Roman in the ruling class would probably have recognised the literary game being played." Atwill maintains he can demonstrate that "the Roman Caesars left us a kind of puzzle literature that was meant to be solved by future generations, and the solution to that puzzle is 'We invented Jesus Christ, and we're proud of it.'"

At this point, it sounds like we're talking about a 2nd rate Da Vinci Code. So my question here is a little meta: is this what historians would call a "red flag" for badhistory?