I cannot condone the ideas that were being spoken in this group, but they do have freedom of speech and freedom of religion. And, of course, the right to bear arms is protected, along with the concept that it allows a tyrannical government to be overthrown by design. This may be their defence, although the killing of cops to further this goal is clearly misguided and wrong. And it's worth noting that there is a boiling point that many Americans will be willing to fulfil the second amendment's other purpose. Again, these are symptoms of a much larger problem that is only getting worse as the government refuses to change course.
Historically, these constitutional protections are afforded every citizen who is not serving in the military. Not foreign nationals or combatants. The difference in this case from Ft. Hood or 9/11 is clear, these people had every right to be locked up for suspicious activities.
If they did intend to go through with their plans, it would make more sense for law enforcement to wait until the attack was imminent before arresting them, as to be better able to prove a conspiracy. The arrest now seems to serve political motives more than legal.
It's also interesting that these are "christian extremists" , when Maj. Hassan's religion was barely mentioned, officially or otherwise, even though it was his prime motivation.