Noah has been banned in Indonesia, Qatar, Bahrain and the United Arab Emirates because it could offend Muslim viewers by depicting a prophet.
Aronofsky, 45, who grew up to be an atheist, has also endured criticism from Christians. But, the criticism was coming largely from people who had not seen his film, which stars Crowe as Noah, Connelly as his wife Naameh, Hopkins as Methuselah and Watson as the orphan, Ila.
"People who were nervous, it was before they saw the film," he said.
"All of the people that have been nervous, we've showed the film to them and we have even received a few apologies about peoples' first reactions because they were judging before they saw it.
Watch: New trailer: Noah
"But, now people are going to see it and everyone seems to be getting excited by it and supporting it."
Hopkins said the story's message was a relevant one. "This is a powerful story," he said.
Early reviews of Noah have praised Crowe's performance and director Aronofsky's ambition but were mixed in their verdicts.
Variety's Scott Foundas said: "If Aronofsky's US$130 million, 137-minute movie ultimately feels compromised at all, it's less by studio interference than by its director's own desire to make a metaphysical head movie that is also an accessible action blockbuster ... Noah does not always sit easily astride those competing impulses, but it is never less than fascinating - and sometimes - dazzling in its ambitions."
Foundas also praised Crowe's Noah as "superbly played".
Todd McCarthy of the Hollywood Reporter wrote: "Aronofsky wrestles one of scripture's most primal stories to the ground and extracts something vital and audacious, while also pushing some aggressive environmentalism."
Movie preview
What: Biblical epic Noah.
Who: Written and directed by Darren Aronofsky. Stars Russell Crowe and Anthony Hopkins.
When: Opens in New Zealand cinemas today.
- AAP