What Ever Happened to Innocent Until Proven Guilty?

"Police to screen CTA train passengers for explosives"
Current Event of October 23, 2014
From Chicago Tribune

What Police Expect to Find

          Authorities in Chicago are going to start searching train passengers for explosives as a precaution. They are going to conduct random searches at checkpoints. Passengers are asked to hand over their bags so that they can be checked. If they agree, and give up their luggage, the police use a cloth to swab the outside of the bag. They then proceed to scan the cloth to see of there is any explosive residue. If the passenger refuses to let the police officer check for explosives, then the authorities have the full right to keep the passenger off the train. Chicago has taken a less evasive approach to searching for explosives. Some cities, like Los Angeles, actually open up people's baggage instead of swabbing the outside. The city of Chicago claims to want to protect the privacy of its train riders. 
           Even though the methods to prevent explosives from being carried on trains varies from city to city, the intent behind it is the same nationally. The new villain in America is terrorism. It makes sense after events such as the 9/11 attacks and the Boston Marathon Bombings, that the majority of the public would be concerned about explosives and the proper way to avoid further attacks. However, police officers seem to be encroaching on people's right to privacy. If a person refuses to let the police search their private belongings, they are not allowed to board the train. The reason behind this makes sense, because the federal government's main focus is to stop terrorism. But, whatever happened to innocent until proven guilty? People are suspects as soon as they refuse to give up their right to privacy. They may not be guilty at all, but they are treated the same way as someone who is. There has to be a balance between proper security and the freedom of the common person to go as they please.