I mean that if people are burning Korans with a lot of publicity attached, and the President doesn't say anything, it looks like he's implicitly supporting it. Which is unfortunate, but in our society our elected officials are pretty much forced to comment on everything, because people expect them to and draw all sorts of conclusions when they don't. Especially when people with no official responsibility like Sarah Palin can't STOP commenting on everything.
I don't think it does to many. Though Obama kind of brought that all on himself, being out there campaigning for anything and everything, commenting on so much prior, hell, damn near promising to personally correct all of our life problems during his presidential campaign. Taking the personal stances from the arrest of a Cambridge professor (the police acted stupidly) to the AZ law (being arrested for buying ice cream).
Just to throw something out quickly, Obama could have said something along the lines of "I do not encourage these actions. It was not the Islamic faith that attacked America on Sept. 11 rather a group of extremists which we are continuing to fight against, to protect the rights and freedoms of as many people as we can, including those of this Pastor in Florida."
What Obama actually said comes across as a message of weakness, and certainly what I would consider out of character for any President of this country.