Joining the military may strip you of legal rights, but it doesn't strip you of any human rights. The article is about human rights violations, not whether or not the government has committed a crime in the US legal system.
(Consider more obvious human rights violations protected by law in certain jurisdictions: stoning people to death for adultery, killing someone's entire family for writing an anti-government blog post, the list goes on. The mistreatment of Manning is just another entry in this long list.)
I was married to a soldier for many years. They protect your right to get three square meals a day, to get your mail and to get something like four hours of sleep a day. They will make allowances for behaviors that would normally be termed "insubordination" if you have been awake excessively long (I can't recall the exact number of hours this applies to, possibly 24 hours). There isn't much else you can count on.
I am not saying that justifies torture. But your rights are substantially different in the military. You are officially AWOL if you are late to formation (i.e. Being late to work is a potentially serious crime if they want to make a big deal out of it). You cannot call in sick. You show up for formation and after formation you request sick call. If the doctor puts you on profile and bed rest, you might be excused from work for a few days.
(Consider more obvious human rights violations protected by law in certain jurisdictions: stoning people to death for adultery, killing someone's entire family for writing an anti-government blog post, the list goes on. The mistreatment of Manning is just another entry in this long list.)