The former Bishop of Liverpool believes that football fans "misdirected" their frustrations when booing Prince William and the national anthem.
The Duke of Cambridge - the FA President - was met with jeering and displeasure when he arrived at the cup final ahead of Liverpool's victory over Chelsea.
The prime minister has condemned the move, calling it a "great shame."
However, Liverpool Football Club manager Jurgen Klopp has stood by his fans, saying that they wouldn't be booing without cause.
Fan frustrations stem from the suggestion that voices within their community have been ignored by the state for a long time, much of this linked to Hillsborough Disaster. That event saw 97 football fans killed at a match between Liverpool FC and Nottingham Forest in 1989; 766 people were injured. An inquiry would later criticise police for their actions at the scene and and subsequent cover-ups of wrongdoing.
Despite the distaste shown by Wembley's visitors, Jones - who is chair of the independent panel into the Hillsborough disaster - told LBC that the Queen had been a great supporter of the city.
Speaking on Shelagh Fogarty's show, he said: ""My feeling, listening to the booing during the anthem, was it was misdirected even though I do understand the ongoing hurt and pain that many people feel."
He continued: "The Queen in my time came to the city quite a number of times for the Royal Variety, for the Golden Jubilee, for the regeneration of the city.
"At the 10th anniversary [of Hillsborough] she sent me a message to be read out to the crowd. She sent me a message of condolence and sympathy."