Yes.
https://en.wikipedia.org/wiki/Providing_material_support_for... explains one law under which intellectuals in the US face state harassment and persecution for speaking and writing certain ideas; Tarek Mehanna, who is serving 17 years in prison for translating "propaganda" under this law, is probably the most cut-and-dried case.
But there are many other examples.
Of course, Aaron Swartz faced years of state harassment for his work on PACER, which was entirely legal, and was then hounded to suicide in a follow-on case for downloading academic articles.
Carl Malamud constantly answers baseless legal threats, and sometimes fights in court, in exchange for his continuing work of putting the law online.
TorrentFreak is regularly blocked by one or another Western government for their political advocacy against copyright.
US citizen Anwar al-Awlaki was assassinated by the CIA for his political advocacy of terrorism against the US; his son, 16-year-old US citizen Abdulrahman al-Awlaki, who had no connection to terrorism, was assassinated by the CIA two weeks later.
US citizen Jacob Appelbaum, who has never had privileged access to any classified information, was harassed by the US government for years and is now living in exile in Berlin, due to his journalistic work.
US citizen Laura Poitras, who has never had privileged access to any classified information, was harassed by the US government for years and is now living in exile in Berlin, due to her award-winning documentary films and other journalistic work.
You're probably too young to remember when Jon Lech Johansen was arrested in Norway in 2002 for explaining how to decrypt the DVD copy protection scheme, and gag orders were imposed on periodicals in the US in an ultimately thwarted effort to "unpublish" Johansen's code. And you're probably too young to remember when Dmitry Sklyarov was arrested while visiting the US in 2001 for violating US law by writing Russian software in Russia for his Russian employer. And maybe you don't know about Joe Nacchio, the CEO of Qwest, the only phone company that didn't cooperate with the NSA's illegal wiretapping program — which was then systematically destroyed, and Nacchio sent to prison for six years on trumped-up insider-trading charges.
And you probably don't care about people like US citizen Eric Garner, who was murdered on the street by a gang of policemen for speaking, to a policeman, the idea that he would really appreciate it if the state harassment of him would stop. I say you probably don't care because there's no reason to think he was an "intellectual". But non-intellectuals' lives matter, too, and so does their freedom of speech.
And maybe you hadn't heard that in Texas, ownership of laboratory glassware is now officially considered evidence of a crime — a truly medieval situation, criminalizing amateur chemistry because of the War On Some Drugs. You don't even have to speak or write about your chemistry research to get harassed and persecuted by the state for it. At least they don't burn the alchemists at the stake these days. Instead they send them to prison to be repeatedly raped.
But it's hard to believe you're so dumb you think this kind of thing really doesn't happen.
Speaking of those prisons — did you realize the US currently has 1% of its adult population in prison? And nearly 2% of its adult male population? And that this is a number almost unprecedented in human history, except for situations like the Holocaust and the Khmer Rouge? * Communist-era East Germany couldn't hold a candle to that level of repression in quantitative terms. Iran, which has a terrible human rights record, has about a third the number of prisoners the US does. Your chances of going to jail without ever having committed a crime are a lot better in the US than in Iran. Unless you're white.
And this thing about how Iran tortures prisoners — I don't know if you missed it, but torture is the official policy both of the Bush administration and the Obama administration.
Do you really think there's no persecution for speaking certain ideas? What do you think would happen if you uploaded a Daesh beheading video to YouTube with your approving commentary?
* Situations like the Holocaust, the Khmer Rouge, and, much to my surprise, the current Seychelles Islands' War On Piracy. The kind with boats, not the kind where some jackass erases your birthday party video from YouTube because you didn't pay the royalty for Happy Birthday.