England Test captain Root says the racism scandal at his county side has "fractured our game and torn lives apart".
Root called for "change and actions".
But when asked if he had seen any racism at Yorkshire, Root said: "Not that I can recall, no... but it's clear things have happened at the club."
A report found former Yorkshire player Rafiq was a victim of "racial harassment and bullying" but the club said they would not discipline anyone.
Yorkshire chief executive Mark Arthur resigned on Thursday, with the scandal continuing to engulf the club.
His exit follows the resignation of chairman Roger Hutton last Friday.
Rafiq tweeted in response to Root's comments: "Disappointed is not even the feeling. Incredibly hurt. But uncomfortable truths are hard to accept it seems."
Root has spent his entire county career at Yorkshire, making his second-team debut in 2007 before progressing to the first team in 2009.
"I just want the sport to be a place where everyone is enjoying it for the beautiful game it is and feels equal and safe," said Root. "We need to educate, unify and reset.
"I want to see change and actions that will see Yorkshire County Cricket Club rise from this with a culture that harnesses a diverse environment with trust across all communities that support cricket in the county.
"I will reach out to YCCC new chair Lord Patel to offer support, however I'm able."
Rafiq, who was born in Pakistan and moved to England aged 10, played the majority of his career at Yorkshire, between 2008 and 2018.
He captained England teams at youth level and also captained Yorkshire in 2012.
However, in September 2020, following an initial interview with Wisden,
Rafiq told ESPN Cricinfo
"institutional racism" encountered while at the club left him close to taking his own life.
He told BBC Sport he dreaded "every second" of his career and that a team-mate used a racially offensive term linked to his Pakistani heritage.
Yorkshire cricket racism scandal - how we got here
Rafiq should be 'praised' for bravery, says Yorkshire chair Patel
No-one at Yorkshire 'racist' but culture 'locked in the past' - Hutton
Yorkshire launched a formal investigation into Rafiq's allegations in September 2020 and then-chairman Hutton said the club would be carrying out a "wider review" of their "policies and culture".
In August 2021, three days after Yorkshire received the findings of the independent report carried out by law firm Squire Patton Boggs, they admitted Rafiq was "the victim of inappropriate behaviour" - something Rafiq said was downplaying racism - and offered him their "profound apologies".
The report summary said Rafiq was the "victim of racial harassment and bullying", with seven of the 43 allegations upheld, although the club said they could not release the full report for legal reasons. They said there had been insufficient evidence to conclude the club were institutionally racist.
Rafiq questioned what punishments had been handed out to former players and a coach who had been found guilty of using racist language. He also questioned the validity of the investigation.
Root, who was talking at England's Ashes preparation camp in Queensland, Australia, added: "It hurts knowing this has happened at YCCC so close to home.
"It's my club that I care passionately about it. I've spent a lot of time reflecting.
"There is no debate about racism, no one side or other. It is simply intolerable."
Ex-Pakistan seamer Rana Naved-ul-Hasan was the second first-team player to allege racism at Yorkshire, saying "systematic taunting" occurred at the club.
Former Yorkshire academy players Irfan Amjad and Tabassum Bhatti have since shared their experiences of suffering racism while at the club.
Rafiq and senior Yorkshire officials will give evidence at a Digital, Culture, Media and Sport select committee hearing on 16 November. Former Yorkshire chairman Hutton will be questioned by MPs, along with chief executive Mark Arthur.
Last Friday, Hutton was one of several board members to resign over the club's response to racism experienced by Rafiq.
On Monday, new chair Lord Patel said Rafiq "should be praised" for his bravery and "should never have been put through" Yorkshire's racism scandal.
On Tuesday, Yorkshire announced head coach Andrew Gale had been suspended as part of an investigation into a tweet he sent in 2010, and that director of cricket Martyn Moxon was absent from work because of a stress-related illness.
Arthur's departure as chief executive followed on Thursday, with Lord Patel saying: "We thank him for his tenure.
"This is an important moment for the club, which is ready to move forward with new leadership, which will be vital in driving the change we urgently need.
"We know there is still much work to be done and more difficult decisions to be made. We need to rebuild the trust of the fans, the cricketing world and the public."
Root, who will lead England in the first Ashes Test on 8 December, added: "We have to find a way to move forward and make sure this never happens again. In my opinion, this is a societal issue and needs addressing further afield than just cricket.
"That being said, we, as a sport, all have to do more. How can we all help shape things moving forward positively? What can everyone from myself, the ECB, counties, players, officials and others in the sport do to improve the state of the game?
"I certainly don't have all the answers, but I think we need to educate more and earlier; we must call it out straight away and have our eyes and ears open more.
"Inclusivity, diversity and anti-discrimination is something over the past few years the England teams I have been involved in have spent a lot of time talking about and are very passionate about improving and making a big difference.
"It's a big part of our culture, and we want to celebrate our diversity. We are representing England, and in that, we are representing the multicultural society we live in. We want all the fans to be able to enjoy what we do on the field and feel proud about who's representing them."
Rafiq report timeline
2 September 2020: Following an initial interview with Wisden, ESPN Cricinfo publish an article with Rafiq in which he claims "institutional racism" at Yorkshire County Cricket Club left him close to taking his own life.
3 September 2020: Yorkshire say they have launched a "formal investigation" into the claims made by Rafiq and chairman Roger Hutton says the club would be carrying out a "wider review" of their "policies and culture".
5 September 2020: Yorkshire asks an independent law firm to investigate racism allegations against the club by Rafiq.
13 November 2020: Rafiq says he hopes to bring about "meaningful change" after giving his first statement to the inquiry.
15 December 2020: Rafiq files a legal claim against Yorkshire "claiming direct discrimination and harassment on the grounds of race, as well as victimisation and detriment as a result of trying to address racism at the club".
2 February 2021: Yorkshire threatens a lifetime ban for anyone found to have made threats against Rafiq or his family and legal team, after ESPN Cricinfo shows the club messages sent to Rafiq's legal firm.
17 June 2021: An employment tribunal case between Rafiq and his former club Yorkshire fails to find a resolution. The independent investigation into his racism allegations remains ongoing.
16 August 2021: Yorkshire receive the findings of an independent investigation into the racism allegations and, two days later, the England and Wales Cricket Board (ECB) asks for a copy.
19 August 2021: Yorkshire, yet to release the findings of the report at this stage, admit Rafiq was "the victim of inappropriate behaviour" and offer him "profound apologies".
Rafiq accuses Yorkshire of downplaying racism by calling him the victim of "inappropriate behaviour".
8 September 2021: MPs tell Yorkshire to publish the findings of the report "immediately".
10 September 2021: Yorkshire release the findings of the report, which says Rafiq was the "victim of racial harassment and bullying" and seven of the 43 allegations made by the player were upheld by an independent panel.
According to Hutton, the report said there was "insufficient evidence to conclude that Yorkshire County Cricket Club is institutionally racist".
Yorkshire released a summary of the panel's report and recommendations, but said the full report could not be released for legal reasons "in relation to privacy law and defamation".
8 October 2021: Yorkshire miss a deadline to send the full report to Rafiq and his legal team after BBC Sport understands an employment judge ordered the club to release it in full by Friday, 8 October.
13 October 2021: Rafiq then receives a heavily redacted version, while the ECB says it is still awaiting the full report.
28 October 2021: Yorkshire say they carried out their own internal investigation after the findings in the report and concluded that "there is no conduct or action taken by any of its employees, players or executives that warrants disciplinary action".
2 November 2021: The Digital, Culture, Media and Sport select committee calls on Hutton to appear before it to answer questions about Yorkshire's handling of a report into Rafiq's allegations of racism.
MP Julian Knight, chair of the DCMS select committee, calls on the board of Yorkshire County Cricket Club to resign after a leaked report emerges apparently containing details of the investigation into the treatment of Rafiq.
A story published by ESPN says the report had concluded that a racially offensive term used towards Rafiq was regarded as "banter".
Knight makes his comments after health secretary Sajid Javid calls for "heads to roll" at Yorkshire and said if the ECB did not take action "it's not fit for purpose". He further states in a Twitter post that the term allegedly used to describe Rafiq was "not banter".
The ECB announces it will conduct a "full" investigation into the situation.
3 November 2021: The date of the DCMS hearing is scheduled for 16 November and Rafiq is called to give evidence in person, along with senior Yorkshire officials.
Several sponsors, including primary sponsor Emerald Publishing and Yorkshire Tea, end their partnerships with Yorkshire County Cricket Club.
Current Yorkshire batter Gary Ballance releases a lengthy statement expressing regret for using a racial slur against former team-mate Rafiq.
4 November 2021: The ECB board suspends Yorkshire from hosting international matches.
Kit supplier Nike ends a four-year deal, announced in March 2021.
Former England captain Michael Vaughan says he was named in the report but "totally denies any allegation of racism".
5 November 2021: Yorkshire chairman Roger Hutton resigns over the club's response and apologises "unreservedly" to Rafiq. Two further board members also quit and a fourth will step down in the near future. Lord Kamlesh Patel of Bradford is appointed as a director and chair of the club.
Former Yorkshire player Rana Naved-ul-Hasan says he heard an alleged racist comment made by Vaughan to a group of Asian players.
8 November 2021: Speaking for the first time since his appointment, Lord Patel apologises to Rafiq and says the club have settled the employment tribunal with their former player.
Irfan Amjad, a former Yorkshire academy player, says he was racially abused by a member of staff at Yorkshire, aged 16.
9 November 2021: The government says it is ready to "step in" if Yorkshire and the ECB do not take "real action".
Another academy player Tabassum Bhatti says he suffered racist abuse at the club as a 14-year-old.
10 November 2021: Yorkshire say they will launch an investigation after the club's head of human resources calls a supporter "a coward" and accuses the fan - and Rafiq - of "waging a campaign" against the club on social media.
11 November 2021: Yorkshire chief executive Mark Arthur resigns.