One of the groups which has been particularly critical of the campaign is FootballvHomophobia, which has taken umbrage with some of the language used to promote the laces project.
It is particularly concerned by the innuendo used and believes the campaign's tag line "Right behind Gay Players" is unhelpful in the battle against homophobia.
A statement read: "Our discomfort is with the reliance on sexual innuendo and stereotypes about gay men and anal sex, as exemplified by the tag line 'Right behind Gay Players'.
"As an initiative with a strong focus on education, 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.
" 'Rainbow Laces' may have an important short term advantage of drawing attention to the issue of homophobia in football, but this needs to be followed in the long term with an informed and sensitive discussion around the contested nature of what constitutes discriminatory, offensive language as opposed to acceptable banter."
However, Paddy Power said it had taken advice from Stonewall "to ensure the tone of this campaign is right."
"We've had a lot of positive support this week from the public in general and other bodies like the Gay Football Supporters' Network," its spokesperson said.
"We sent the laces out to clubs three days before the campaign went live to give them the opportunity to discuss this internally. The laces were accompanied by a full explanatory letter and invitation to get in contact with us if they had any questions.
"It's pretty sad that some of the powers-that-be deem this not enough notice when it's a simple case of players choosing whether or not they'd like to wear a pair of rainbow laces."
Paddy Power also brushed off criticism that its involvement had hindered the campaign.
"The rainbow laces we've provided are simply rainbow-colored and not branded, so they do not breach any FA rules or clash with any commercial deals," it said.
"It's a real shame that some in the game are using our involvement as a pretty weak excuse to prevent players from making a choice on whether they want to lace up to show their support."
However, the opposition has not put off other sports stars supporting the campaign, with English rugby players also getting in on the act.
James Haskell, an England international who plays for club side London Wasps, plans to wear the laces this weekend while former football player turned television presenter, Gary Lineker, has also spoken of how he will boast the rainbow colors.