Child's Play is no longer accepting donations from the Retake Mass Effect movement because Penny Arcade were worried that people thought they were donating to a fund that would result in a different ending for the series, rather than to a charity for sick kids. People were also wrongly assuming that Penny Arcade or the Child's Play charity were somehow in support of the petition, both incorrect assertions.
Anabel Martinez, the organiser of Full Paragon – a Mass Effect-focussed campaign raising money to get kids reading – thinks that it goes deeper than that, and blames the press for their negative view of the whole thing.
“When a lot of the press took a sour approach to the Retake fundraiser, several Mass Effect fans were drawn away from the inherently positive fundraising effort, because of the negativity that was generated by many gaming journalists,” she told BeefJack.
“Instead of the focus being on helping charity, the focus did become about the group’s participants wanting to put pressure on BioWare to change or correct the ending.”
“Ultimately, what damaged Retake’s fundraising was the media and press taking it as ‘jumping on the good-cause bandwagon,’ even if it really wasn’t.”
I don't think I saw anybody saying that raising over $80,000 for charity was a bad thing, I think it's fair to ask whether the fundraising would have even been started (let alone that amount raised) if not for the petition to change Mass Effect 3's ending. It had a positive outcome, but it's fairly obvious that the fundraising was done to draw attention to the cause, not the other way round.