That's never certain: The FCC regulates by way of Congress' authority, and Congress can change that authority any time it likes (and the President concurs) through the normal legislative process. They can also make trouble for future FCC appointments, call FCC members in for hearings, and otherwise make the FCC's life miserable.
It's absolutely one of the things that limits the FCC's freedom of action.
IMHO, this is simultaneously a political move (nobody loves Comcast), an ideological move (President Obama almost certainly believes that additional regulation in this area will be good for consumers) and a negotiation tactic (the more the broadband providers are worried about Title II, the more willing they'll be to support FCC neutrality regulation short of that).