Who is saying they aren't allowed to question the President or anyone?
Next time someone yells "fire" in a crowded theatre, should they claim freedom of speech even though they may have created a panic?
And if someone comes to a party at your house and brings a friend of theirs that you did not invite, and said friend insults you, are you going to let them stay because of their first amendment rights?
I think the issue is security. In an event like a political convention or rally, I believe the party in question, be it the GOP, the Dems, the Libertarians, or whomever, has the right to restrict access to the facility. Especially in this day and age when any ordinary joe schmoe could be a Mohammad Atta.
Again, who is saying the protestors aren't allowed to question the President? They may not be able to question them at MSG at the convention, which is a private event, despite the media coverage, but they are more than welcome to do so in other venues.