It seems the NoScript author sneakily added some whitelist rules to people's Adblock Plus list so ads on his website are not blocked. This might even have been OK by most people if only he had been frank and up-front about it. But he went further: he also *patched the AdBlockPlus code* to enable supporting ads on the NoScript site (see all the angry comments on the extension's page). This suddenly makes it malware, as modifying code you are not supposed to touch is really Not Done.
The public outcry now seems to have resulted in an update which removed the offending code, but this surely has resulted in a distrust of the particular extension which people used to love.