Yup, he is attacking a group for exercising their freedom of speech. Like I said earlier, it sounds like you think the President should not have a personal opinion on what a group does. You think the president should put the same effort in defending the community center as he should defending a Koran burning session or a KKK rally.
Let me see if I can explain this.
There was a scene I remember from the TV show The West Wing.
President Bartlett invited an old confidant, I think it was his old priest, to the oval office to advise him on something. When the guy asked if he should call him Joe or Mr President he explained that, in that room, everyone called him Mr President so that he would never forget the responsibility he has as the president, and that he literally makes life and death decisions every day.
Obama is not acting like a president when he weighs in on two issues that are, at their core, exactly the same. If he, properly, claims that we need to respect everyone,s right to practice their religion I will respect that. (A respect he promptly looses when he claims he never talked about the wisdom of the action.)
If he then talks about how bad it is for another group to practice their religion, because it upsets others, then I will call him on it.
Is he entitled to a personal opinion? Yes.
Is he allowed to express that opinion to the press? Again yes, but it shows poor judgment.
Is he allowed to let that opinion to prevent him from doing his job? No, and that is what he is doing here. His job requires him to support, and defend, the Constitution. If he picks when he does that, and when he does not, he is not doing his job.