Folau sparked a Twitter backlash by revealing he will not support gay marriage, becoming the first high-profile sportsperson to have publicly announced their opposition.
It came after numerous sporting organisations -- including the Australian Rugby Union -- declared their support for a 'yes' vote in the government's postal survey.
Folau's views are also at odds with outspoken former Test skipper David Pocock while current captain Michael Hooper has also voiced his support for gay marriage this week.
In camp with the Wallabies in Canberra ahead of their Rugby Championship Test against Argentina, Cheika said Folau had the right to voice his views and didn't believe it would cause a rift among his players.
"I don't see how it could make a division within the team," Cheika said.
"This is a national issue and, for everyone, respect is king.
"A lot of people have different opinions about lots of things in our team and our team is a reflection of Australia.
"And definitely within our team culture ... there's been a real camaraderie and internally we've got 100 per cent respect for everyone's opinions on all matters."
Cheika wasn't concerned that Folau, who is a devout Christian, would be distracted by the response to his comment, with more than 3500 replies on Twitter.
"You'd have to think he'd know that that would happen," Cheika said.
Former Welsh rugby great Gareth Thomas, who is gay, used the middle finger emoji to respond to Folau's tweet.
Ex-Australian cricketer Shane Watson tweeted a link to a newspaper story about Folau and his netball star fiancee Maria Tutaia and wrote "Love should have no boundaries".