Well, for one, there is a notable difference between the nature religions, which claim that God or gods are found in nature, and a religious tradition like the Hebrew one, which proposes a God that transcends nature and is described in historical narrative. The rejection of nature worship is one of the prominent features of the Judeo-Christian religious tradition.
The movie lacks any sources versed in the history of any religion, and thus primarily deals in claims which are credible only to the credulous. It's like the atheist version of Creation Science.
For example, the movie makes several statements about the Egyptian god Horus which are blatantly false, such that he was born on December 25th, born of a virgin, that a star in the east appeared when he was born, that he was worshipped by kings, that he was a teacher of 12, that he was called the lamb of God, and that he was crucified. It claims that this non-existent version of the Horus myth was the original one from 3000 BC, which is curious since there are no known sources on Horus from that far back.
It also claims that the 12 disciples represent the 12 signs of the zodiac, as opposed to the 12 tribes of Israel, from the Genesis narrative, which had absolutely nothing to do with astrology.
It claims that A.D. 1 represents some new age under the zodiac, which is fine since Jesus was born around 6 B.C., and the calendar represents an error by a later scholar.
It claims that Christian worship on Sunday is pagan in origin, despite the copious evidence of the debate between church fathers on which day should be the day or worship (Sabbath or the day following?) which has to do with the relationship between the tradition of temple worship and the tradition of the Eucharist. It has nothing to do with sun worship.
It claims that the Christian "fish" symbol is zodiacal, rather than a symbol of a Greek anagram for Jesus (i-ch-th-u-s = Iesous CHristos THeou Uios Soter).
The movie claims that "Son" of God might actually really mean "Sun" of God, as though the language of Judea or the Roman Empire were modern English.
The whole idea that Christianity from its outset was a tool of the elites to control the people is historically ridiculous, insofar as it was a religion which outside of its stronghold in western Anatolia was a tiny minority religion until the Edict of Milan in 313. It was intermittently persecuted by local rulers (though not systematically throughout the Empire as is often believed), because Christians refused to confess Caesar as Lord and Savior, and therefore were regarded as seditious. There are volumes of writings do enting these first three centuries.
You can't claim the so-called intellectual high ground as a skeptic while believing a movie whose claims about Christianity are devoid of scholarship even to the level of reading Wikipedia entries. Latching onto such tripe betrays one simply as an anti-religious bigot with an axe to grind.