The anthem, believed to have been written by a slave in the mid-19th century, became a mainstay with England supporters in the 1980s and the RFU said last month that it was reviewing its use following the Black Lives Matter protests.
"It's an awareness and education piece," Jones told Sky Sports.
"I remember coming in the 2000s and hearing the song when our scrum was under the pump. It didn't resonate to me, that it was involved in things that possibly aren't too flash.
It was a rugby song but given that people now have that awareness ... it's probably a choice they have got to make. If they are educated enough and aware enough, they'll make the right decision, but that's not for me to tell them.
England rugby fans
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The novel coronavirus pandemic has cast doubt over the future of Super Rugby, with New Zealand pushing for an eight-to-10 team competition that would exclude South Africa and Argentina but include teams from Australia and one from the Pacific.
South Africa are looking to fill the 2021 vacuum with their own competition which would include Argentina's Jaguares and possibly the Cheetahs and Southern Kings. Jones believes strong domestic competitions are needed to raise the standards of the game.
"The main thing is, and I think it's shown, is that people want a strong domestic competition. And it's probably fallen away a little bit," he said.
New Zealand's Super Rugby has shown that people want to see the best against the best ... I think the task for each country is to make sure their domestic league is the highest level of competition, and if you do that, fans will come and watch.