Can someone clear up the recent legal mess with poker websites PLEASE?

Okay so online gambling is not illegal, so why were the sites shut down, how were they SUPPOSED to operate, how can online gambling be legal but it's almost impossible to get money out of websites in the US because how they transaction it is illegal? why would online gambling be legal in the first place if there is no legal way to manage the money, please someone explain this clearly and not vaguely.