These things have happened in the United States.
A man was arrested for criticizing Dick Cheney to his face. He was charged with assault. This was in Colorado.
A man was arrested for flying an upside down American flag. This was in Iowa.
A man was arrested for wearing a t-shirt that said "give peace a chance" in a mall. This was in New York State.
A man was arrested for wearing a Veterans For Peace t-shirt in a V.A. Medical Center. The man was a veteran. Illinois.
A man was arrested for holding a sign reading "Honk if you want Bush Out". Michigan.
A 15 year old boy was arrested and assaulted by a police officer and two security guards after refusing to remove a t-shirt with the words "stop snitching" on the front, and "you have the right to remain silent" on the back. The police officers used mace. Maryland.
A man who fought for the rights of airport baggage screeners was visited at home by the FBI and questioned about terrorism. California.
A man wearing a t-shirt with Arabic writing and the words "We will not be silent" was forced to change into a different shirt in order to board a flight from New York to his home in California. His story in his own words is here.
Here's some First-Amendment shredding I witnessed first hand. The ACLU published an excellent report (pdf) on New York City's attempts to squelch the massive anti-war protest on February 15, 2003. Scroll through. It's quite an education.
I'm not including on this list civil disobedience protests where people blocked traffic, interrupted speeches or trespassed on federal property.
I'm also not including all the government spying on, harassment of, arrests of and threats against activists, both now and throughout its history.
And, although they weren't protesting, and didn't get arrested, I feel I should mention the two men who were told to stop touching on an Americans Airline flight from Paris to New York. The pilot threatened to divert the flight unless they complied. (Contrary to some reports, they weren't arrested or charged with suspicion of terrorism.) Not sure if this qualifies as "in the United States," but it is a US company.
In most (though not all) of the above cases, the arrested citizen was vindicated in court, often with the help of the ACLU. But, as one commenter pointed out, the arrests achieve the immediate goal of quashing potential dissent, as most people fear arrest. (Many people can lose their jobs, or their right to live in the US, if arrested.)
And, as others have mentioned, despite the judicial exoneration, under the new US laws suspending habea corpus, any one of these harmless people could be declared an enemy combatant - and be made to disappear.