Stonewall, a gay rights charity, joined forces with Irish bookmaker Paddy Power to send the laces to 5,000 footballers around the country - but clubs are angry that they received the laces with no warning or consultation, and are evidently aggrieved at what they paint as an attempt to turn a serious issue into a publicity stunt.
Premier League champions Manchester United, Tottenham and Liverpool are among clubs who have decided to boycott the laces, according to widespread reports, with one Premier League official saying that, "in short, the whole thing has been embarrassing and infuriating."
United and Tottenham issued statements explaining why none of their players will be wearing the laces, with United making it clear that the tie-in with the bookmaker was the sticking point but adding that they will support any future efforts to end homophobia in the sport.
"It is a positive move that Stonewall are now speaking to the League directly, rather than working with a commercial provider on a campaign without involving clubs or players at any stage," United's statement said.
Spurs statement echoed similar concerns: "Whilst the campaign message is positive and one we support, there was unfortunately no prior consultation with ourselves, the Premier League or other clubs," the Tottenham statement read.
"Such consultation would have enabled us to avoid issues in respect of associated third-party commercial entities. We have contacted Stonewall directly and let them know that we are supportive and keen to discuss ways in which we can work together going forward."
Anti-homophobia organisation Football v Homophobia (FvH) has also criticised the initiative, and in particular the slogan 'Right behind gay footballers'.
"Our discomfort is with the reliance on sexualised innuendo and stereotypes about gay men," ," FvH said in a statement on Thursday.
"We feel it is incongruous to run a campaign aiming to change football culture whilst using language which reinforces the very stereotypes and caricatures that, in the long term, ensure that homophobia persists."
Power said the lack of openly gay footballers in Britain did not reflect the reality.
"There's 5,000 professional footballers in the UK and none of them are openly gay - statistically, that's almost impossible," Paddy Power told Reuters in a telephone interview.
"UK government statistics suggest that six percent of people are gay, so we worked out that the odds on no footballer being gay are a quadragintillion to one. That's a one with 123 zeros after it - it's a big number, and it's very, very unlikely that there are no gay players."
Power came up with the idea of manufacturing rainbow-coloured laces to show support for gay players.
"It's subtle, it's not going to affect any player's performance, it's not like guerrilla marketing - it's just a small message of support to show that they don't want homophobia in their game," Power said.
"At the start people, were a little bit worried about putting their hands up, but now there's a groundswell - Joey Barton was the first man to get behind it. Everton's Phil Jagielka has said he will wear them, as will some of his Everton team mates."
Outspoken Queens Park Rangers midfielder Barton has promoted the "Right Behind Gay Footballers" campaign.
"In the 21st century, it's crazy that we're even having this conversation," he said.
"Footballers can show support by putting laces in their boots, and hopefully fans can either put laces in their training shoes and take to the social media sites like Twitter and Facebook."
Despite its global popularity, football has seen very few gay players come out, especially during their active careers as the fear of a negative reaction from coaches, team mates and fans forces them to keep their sexuality secret.
Britain's most famous case was that of former Norwich City striker Justin Fashanu, who came out in a tabloid newspaper in 1990 and committed suicide eight years later.
Former Leeds United player Robbie Rogers quit football and came out as gay after being released by the Yorkshire club this year.
The American's decision to restart his career at Los Angeles Galaxy prompted the New York Times to dub him "the first openly gay man to participate in a prominent North American pro league" when he made his debut against the Columbus Crew in May.
Power said the success of the campaign would not be assessed by the sudden emergence of a number of gay athletes.
"We wanted to make sure we did it in a sensitive way - the campaign is not about outing people, it's not about getting people to come out," he said. "It's about raising awareness of the issue."