So where in the constitution does it say that folks can use megaphones, play music, poop on someones doorstep or car, camp out for weeks on end, create chaos that prevents normal business by both city and private citizens and even blocks city streets. Just because you have the right to protest does not make it right to act uncivilized.
The right to assembly and protest ends when it interferes with the rights of others. In addition, the cities do have a legal right to institute laws requiring assembly permits, etc. Assembly and speech rights do not trump trespass laws.