The mother, who declined to be named, said it showed extremely poor role modelling for such a young person, who was at their most impressionable age.
She said the preschooler and his dad visited the Look Sharp store, in Great King St, late last week, to buy the flag.
"Our son loves flags - we have a growing collection of flags of the world. So they had gone to choose a new one.
"My son saw the rainbow flag and jumped up and down with excitement because he loves rainbows.
"So that was the flag they left with that day."
While the parents support the LGBTQ+ community, the flag was simply purchased because it was the one he wanted.
She said her son liked to have his flags out the window of the car on the drive home, so he could watch them blow in the wind.
But the boy’s actions attracted vitriol from a ute full of people.
"They had only gotten around the corner to the one way when the incident happened.
"It was just around school finishing time.
"All of a sudden, while stopped at the lights, they heard all this commotion of people yelling and screaming.
"My son’s dad realised it was homophobic slurs being directed at them."
The boy’s father said the abuse was "so angry and aggressive" and it carried on as they sped past.
"My son said, ‘that person is very angry’, but thankfully he didn’t realise the abuse was being directed at him.
"Regardless of the fact he just liked it because it was rainbow coloured, this kind of hatred is disgusting."
It was a complete contrast to the earlier connections they had with the community on the walk back from the shop to the car.
They were met with smiles from secondary school pupils, and a busker told the boy that he liked his flag.
The mother believed it was a very important issue to bring to the public’s attention.
"Although I believe Dunedin as a whole is moving in the right direction for equality and acceptance for all, this was a reminder that there is still work to be done."
She put a message on social media, calling out the behaviour of the "absolute embarrassments of society", but was amazed at the number of people who responded negatively.
Due to the "nasty things" that were already aimed at their son online, the parents declined to be named.
"I feel like that is the most responsible thing we can do to protect our son."
