Well, I do understand the free speech implications here - but the protestors also miss a certain point. They are obsessed with telling Bush what they think of him. Bush really doesn't care. However, if they were more saavy, they would play to the media covering the protest and get their opinions out through the media to a larger audience with the power to vote one way or the other in the upcoming election.
I have been herded into "free speech" zones before - and they have a certain benefit of having the press swarming over them, and I've gotten several interviews as a result. So I think the free speech implications here are not nearly as profound as folks wish to make them out to be, if your goal is to be effective to voters instead of trying to make a point to a politican who could care less.
The issue is supporters were allowed to stay, dissenters were threatened with arrest.
And "free speech zones" have no place in this country, period.