It's because an MMO has *yet* to do well on a console. They're afraid of the differences they'll encounter in trying to either combine the worlds populated by PC and console users or keep the worlds separate.
Honestly, MMO's were not common fare before WoW. It takes one good shot to change everyones' minds. The original KotOR changed the way consoles handled RPGs, why can't the KotOT MMO do the same?
Nothing has been officially announced by the publisher but they always planned it as a trilogy and Brotherhood was more an add-on than it was a sequel. So there will definitely be an Assassin's Creed 3 in the future.
Plus considering the cash AC:2 and AC:Brotherhood raked in they'd be crazy not to release it.