The Australian, who was in a standard class carriage from Edinburgh to Manchester the morning after England's 25-13 loss to the Scots at Murrayfield on Saturday, said he would not use public transport again.
"I'll make sure I won't in future. It's as simple as that," Jones told the BBC.
"I'm a human being. I don't consider myself any different from anyone else, so for me to travel on public transport I thought was okay," Jones said.
"I can't because it was shown what happens when I do. That's the world we live in. I was massively surprised. It wasn't comfortable."
Former Scotland captain Gavin Hastings had said supporters of England's opponents want to "rub his (Jones's) face in the dirt" and the former Australia and Japan coach questioned those comments.
"It magnifies that if you're in a position of responsibility you've got to be careful what you say," Jones said.
"Because if you talk about hate and you talk about rubbing peoples' nose in the dirt and all those sorts of things, it incites certain behaviours and are they the sorts of behaviours that we want to see?"
Jones, who has led England to 24 victories in 26 games in charge, attended Manchester United's Premier League game against Chelsea at Old Trafford on Sunday before travelling back to London.
"It's part of the challenge. As an Australian coaching England, there were always going to be challenges and that's just one of them," Jones said.
(Reporting by Ed Osmond, editing by Nick Mulvenney)
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