Is one permitted to donate money to a Rabbi’s organisation if this Rabbi is known to publicly denigrate talmidei chachamim (who disagree with him) on a regular basis?
I don’t know who or what you are referring to, but that is fine. Regarding giving tzedakah, you can choose to give your money to other places and you don’t have to give specifically to that organization if you don’t like some of the actions that the Rabbi does. However we can’t go that far to say that it is forbidden to donate to his organization. If they are spreading torah or doing chesed, what they are doing is still a good cause, unless the cause of the organization is in order to denigrate talmidei chachomim, which I doubt.