J. Edgar Hoover insisted that the Mafia didn't exist, until the Appalachin meeting proved him wrong. Of course Mr. Hoover liked to gamble, and I expect he was willing to overlook a few things as long as he could bet on the horses.
He could also grab a lot of publicity capturing holdup men like John Dillinger or Machine Gun Kelly, and they weren't as tough to find or to deal with as organized crime.
The current administration likes to make people take off their boots in airports, and Duck tape their windows. It doesn't cost them much, and it's much simpler than tracking down Bin Laden and his admirers.