The regime is using a very broad brush to paint opponents as "terrorists". Read the edict again. "anti-Christian" and "anti-capitalism" thought are now markers for "terrorist" activity.

Once you tag someone as a "terrorist", seems the Bill of Rights goes away.

No, it doesn't. First, Padilla wasn't put into military processes because he was designated a "terrorist" - he was designated an "enemy combatant," a participant in an actual military conflict rather than simply committing acts of terrorism. None of that would be applicable to any of the groups you mention in your post.

Second, the Bush Administration ended up bailing on their efforts to hold Padilla without civilian trial and transferred the proceedings against him to civilian criminal court because they were about to lose at SCOTUS after Hamdi v. Rumsfeld. Which case specifically and explicitly found that the Bill of Rights did not "go away" simply because someone was designated an enemy combatant (again, not "terrorist").

It's a category error to assume that because the Administration pushes the envelope (or arguably violates) on the border of civil rights in some areas that means we're living in an environment where there are no civil rights for anyone anywhere. It's just not true.

Articles like the OP make it seem like the Administration is stepping over the line, but that's because folks generally are unaware of the contours of Fourth Amendment protection. You've never had any Fourth Amendment rights to avoid a search or seizure of your belongings at the border. They can look through your stuff, and they don't need a warrant or even reasonable suspicion. That's something the government is simply allowed to do.