Yes, the perceived need for government secrecy has resulted in frequent violations of civil rights in the United States, because the government just reads our emails now, without even having a good reason to. They do not want to tell us that they are reading our emails, so they just do it without telling us or getting a warrant.
There is no doubt that the possibility of civil rights have been violated from time to time in the name of a perceived need for government secrecy in the United States. Not to sound too cynical, but the government has shown a tendency to lookout for its secrets more often than the rights of a few or even one citizen. We have extensive government facilities all dedicated to finding information and keeping said information secret, not as many to insure civil rights of our citizens.
Snowden was the whistle blower that brought attention to the NSA's illegal spying, most recently that it is using Facebook to infect computers and allow them to remotely control web cams and microphones. The abuses of civil rights have been going on for quite some time, though, from the McCarthy era, to the CIA's operation Mockingbird, to the use of Eschelon and Carnivore to intercept phone and internet communications data, to the warrantless wiretapping during the Bush era. The problem is that most people have been in denial for so long, but the abuses are a pervasive and long term, and they will not likely be fixed with the kind of feel good reforms that get pushed through Congress.
I believe the perceived need for government secrecy has resulted in frequent violations of civil rights in the United States. Many Americans feel less free every year as they become a product of the lagging economy and fall further into poverty. Government secrets put these people at odds with the corporations and the government as well. Times are tough.
Under the Foreign Intelligence Surveillance Act, the secret courts were set up to grant wire-tapping requests , data analysis and other types of monitoring to include financial transactions of possible terrorists and spies operating in the United States. This is done with discretion and respect and is not done as if the personal files of an individual are passed between a myriad of eyes.
The Patriot Act passed by Congress following the September 11th, 2001 terror attacks on the World Trade Center and The Pentagon made the establishment of the National Counterterrorism Center and the Department of Homeland Security necessary for the physical protection of all Americans. Our civil liberties are protected until such time that our physical infrastructure is overthrown and controlled by people who wish to harm and destroy the American system of democracy. For this reason alone, there must be "watchdog" organizations in place to circumvent the threats posed by Islamic extremists, such as those groups who perpetrated the terror attacks on the United States.
While some may argue the religion of Islam is one of peaceful intent, the Holy Book of this religion was written by one man intent on implementing conversion to Islam or death. The Qur'an promotes tolerance of other religions only if the followers of other religions pay a special tax or a "jizyah". Under sharia law, this applies to Jews, and Christians, Hindus and Buddhists.
If an American Citizen does not conspire to harm and kill other Americans for the purpose of promoting Islam and Sharia Law, they should have no concern of the telephone numbers they call being recorded, or the frequency of the calls. This is what is recorded, not individual telephone conversations, unless a special warrant is issued by a judge.