Right after 9-11, there were a couple of FBI raids after the obvious nature of the organizations were pointed out to them (even so, the FBI seemed strangely reluctant to do anything about it); the result was that the bank accounts of the "Holy Land Foundation" were frozen, and a few people were arrested. There was another front company (Infocorp, or something similar named; located in Richardson) also involved that was transferring funds to al qaeda in Malaysia. A few of their company officers were arrested, but the organization behind it remains, and is still regularly funding terrorist operations (the initial heat from the FBI made them a little more careful about how they did it).
On the bright side, a lot of the shops and restaurants that used to have the Hamas donation boxes no longer do; so perhaps 9-11 was a wakeup call for at least some Americans.