Among supporters trusts nationwide there is shock and incredulity that Supporters Direct, which has helped save around 50 clubs since it was established in 2000, faces being wiped out by the withdrawal of £1.2m funding from the Premier League.

Richard Scudamore, the Premier League's chief executive, gave a commitment in March 2010 to the Labour sports minister, Gerry Sutcliffe, to fund Supporters Direct and the Premier League was due to sign off a package last week to keep the organisation going for three more years. The money was to come from the Football Stadia Improvement Fund, which is wholly financed by the Premier League.

Then last week the FSIF completely rescinded the funding, saying it was in response to tweets posted by Supporters Direct's chief executive, Dave Boyle, and the organisation's failure to deal with them seriously enough.

Boyle posted his tweets, which contained swearing, while celebrating AFC Wimbledon's promotion to the Football League on 21 May, one of his and Supporters Direct's greatest achievements. He apologised, withdrew them and has resigned – bringing to a sad end a major contribution to football.

On a shoestring, often short-term, insecure budget, Boyle and his staff of only nine developed a democratic model for mutual fan involvement, via supporters trusts which have been formed at 180 clubs in football and rugby league. Supporters Direct advised fans how to grapple with legal and financial horrors, often in existence-threatening crises, to work with other stakeholders and, crucially, how to raise money – as well as campaigning more widely for supporter involvement.

Supporters Direct has received £4m in funding since it was established 11 years ago and calculates its associated trusts have raised £26m, mostly directly for clubs, from share issues, fundraising and membership.

In 2002 the organisation was deluged by cries for help from fans of clubs where years of mismanagement tumbled into death knells with the collapse of ITV Digital and its Football League television deal. Among the clubs where volunteers formed trusts, then played significant roles in the clubs' survival were Lincoln City – an early pioneer – Chesterfield, York City, Bury and Notts County. Exeter City, taken over by their trust after two former directors had run the club insolvently, are still wholly owned democratically by their fans and now in League One.

The rejuvenation of Swansea City, dying at the Vetch Field in 2001, followed unstinting work by the supporters trust, and the local council built the new Liberty Stadium once, with the trust, stability had been restored. Newly promoted to the Premier League, Swansea are still 20% owned by the supporters trust, which has an elected representative, Huw Cooze, on the club's board. Supporters Direct has also worked with supporters of the biggest clubs, most notably Manchester United, Liverpool, Newcastle United and Arsenal, to form trusts either campaigning against damaging ownership or seeking a more active role.

The prospect of all that work being obliterated due to some tweets by the chief executive after 11 years' committed service defies balance and a reasoned approach. It was always an odd fit for the Premier League to be asked to fund an organisation whose philosophy – supporter ownership – looks at odds with elite clubs owned by oligarchs, leveraged buyouts, an Indian chicken company and other plutocrats. The Premier League denies it has seized on this as an excuse not to fund Supporters Direct, claiming it has terminal concerns about the organisation's governance. However, the decision, following 15 months of drawn-out discussions and a track record of excellent work, was made summarily, without prior warning.

The FSIF said in a statement: "The funding will still be available to the broader supporters' trust movement." However, this only increases the impression of a decision made too hastily, by a three-man FSIF panel chaired by the Premier League's director of policy Bill Bush, and the three-man board, on which Scudamore sits.

Trusts mostly require intensive help and advice, often in a fast-moving crisis, and Supporters Direct has developed structures, practices and procedures which all trusts can follow. It looks highly inefficient and unworkable to fragment that expertise into 180 solitary trusts filling in funding applications, with no central body giving advice. Just two weeks ago, the FSIF was convinced of Supporters Direct's value and preparing to fund it. Now it appears to be saying some ill-advised tweets have abolished the need for any organisation to fulfil this role.

That does not speak of considered, independent thinking at the FSIF or Premier League, which is, after all, still a competition for only 20 clubs, yet which appears incrementally to be controlling all of football, including the existence of its supporter groups{jcomments on}.