The problem is not about whether the president can make recommendations to the FCC, independent agency or not.

The problem is when there's a perception that a president's political agenda colors or could be seen as coloring a decision, especially one as business-unpopular/political as the Net Neutrality ruling, and thus makes his recommendations suspect.

There's nothing to prove that Obama did anything more than issue a statement in favor of it, and given the public support for the ruling, it's hard to believe that his late-stage, tacit support means that he suddenly was manipulating the FCC into anything. If anything, it shows that his administration had little choice BUT to support it, and Obama came out in favor of it because Tom Wheeler was in all likelihood going to rule in favor of the companies he lobbied for while there were major players against it.

I can understand the fear that a lot of people have: If the Obama administration is willing to do nothing about NSA surveillance, is willing to call for and pass extensions/expansions of the Patriot Act, and basically act against the best interests of the average citizen, then why is he suddenly supporting a bill which seemingly gives the people everything they demand? It's a fairly reasonable, if not a bit naive, state of mistrust.

What remains to be seen is how this comes out in the long run. We may get lucky, and the cable companies will improve their service and improve what is available. We may also get lucky and see more competition appear. I'm not hopeful, however, because I think while we'll get away from throttling and filtering of what we have now, over time the cable companies will see even less incentive to offer faster speeds or better connections. I'm half convinced we'll just see a stagnation in the market over time since they can no longer treat it as a luxury service demanding competition. I hope I'm wrong.